LOCUS       NZ_CP039281             4018 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg strain
            CFIAFB20170119 plasmid pGTAFD2016-MI-0253.2, complete sequence.
ACCESSION   NZ_CP039281
VERSION     NZ_CP039281.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10501886
            Assembly: GCF_004798765.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Senftenberg
  ORGANISM  Salmonella enterica subsp. enterica serovar Senftenberg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4018)
  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  JOURNAL   Unpublished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 4018)
  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. 4.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 60.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/29/2023 04:03:44
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,075
            CDSs (total)                      :: 4,955
            Genes (coding)                    :: 4,774
            CDSs (with protein)               :: 4,774
            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)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 53 of 181
            Pseudo Genes (incomplete)         :: 140 of 181
            Pseudo Genes (internal stop)      :: 28 of 181
            Pseudo Genes (multiple problems)  :: 34 of 181
            Pseudo Genes (short protein)      :: 1 of 181
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039281.1.
            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..4018
                     /organism="Salmonella enterica subsp. enterica serovar
                     Senftenberg"
                     /mol_type="genomic DNA"
                     /strain="CFIAFB20170119"
                     /serovar="Senftenberg"
                     /isolation_source="food"
                     /sub_species="enterica"
                     /db_xref="taxon:28150"
                     /plasmid="pGTAFD2016-MI-0253.2"
                     /geo_loc_name="Canada"
                     /collection_date="2017"
                     /collected_by="CFIA"
     gene            join(3810..4018,1..4)
                     /locus_tag="EIP70_RS25715"
                     /old_locus_tag="EIP70_26030"
     CDS             join(3810..4018,1..4)
                     /locus_tag="EIP70_RS25715"
                     /old_locus_tag="EIP70_26030"
                     /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_034169353.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            1194..1517
                     /locus_tag="EIP70_RS25730"
                     /old_locus_tag="EIP70_26045"
     CDS             1194..1517
                     /locus_tag="EIP70_RS25730"
                     /old_locus_tag="EIP70_26045"
                     /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_024191642.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1726..>2160
                     /locus_tag="EIP70_RS26365"
                     /pseudo=""
     CDS             1726..>2160
                     /locus_tag="EIP70_RS26365"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            2195..2680
                     /locus_tag="EIP70_RS25740"
     CDS             2195..2680
                     /locus_tag="EIP70_RS25740"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_061390563.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2684..2899
                     /locus_tag="EIP70_RS25745"
     CDS             2684..2899
                     /locus_tag="EIP70_RS25745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_072048928.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3028..3555
                     /locus_tag="EIP70_RS25750"
                     /old_locus_tag="EIP70_26055"
     CDS             3028..3555
                     /locus_tag="EIP70_RS25750"
                     /old_locus_tag="EIP70_26055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016246513.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     Typing          904..1081
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          complement(434..954)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.564"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1508..2991
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgaaagagt ggattcactg taaaacaaca gtcatttttt ggacaacact gtctatatac
       61 gtactcatat gtttcacagt gtcgtatgtt ggagtctatg ttacgtacgt tgcagggcct
      121 attttgttag ttacaggcat tcttgcatgg cttacgaaac ctagctgtaa tccaaagtga
      181 ctgggctaga cgaactttat ccccccataa aacccgcttt tttaaacgga tcttcttgag
      241 atcattcatg gagaatcgta atctcttagc actgtaaacg aaaaaaccgc ccagcaaggc
      301 ggttttttcg aaggttctca gagcagcaac tctttgaacc gaggtaactg gcttggagga
      361 gcacagtcac caaaacttgt cctttcagtt tagccttaac cggcgcataa cttcaagact
      421 aactcctcta aatcagttac cagtggctgc tgccagtggc gttttgtcgt gtctttccgg
      481 gttggactca agtcgatagt taccggataa ggcgcagcgg tcggactgaa cggggggttc
      541 gtgcatacag tccagcttgg agcgaactgc ctacccggaa ctgagtgtca ggcgtggaat
      601 tagataaacg cggccataac agcggaatga caccggtaaa ccgaaaggca ggaacaggag
      661 agcgcacgag ggagctacca gggggaaacg cctgggatct ttatagtcct gtcgggtttc
      721 gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg agcctatgga
      781 aaaacggcaa cgccgcatcc tttttccgcc ctttctgatt gatttccgct tagtctcttt
      841 atccagccat tcgtaagctg gcaacgcccg ccgcagtctc acggcaggag cgcagcgacc
      901 gagtgagcga ggaggcgtca tttcaccggg atctgcattt cgcacttacg ccccacagca
      961 gcattttctc cctgccacat gaagcacttt cctgaatccc cactccgatt taccatgtta
     1021 agccagtata cactccgcta gcgctacgtg actggttcag ggctgcgccc cgaaacccgc
     1081 tgaaaagtac tgccgcgccc tgcgggcttg cccaacaccg ctccggacag gaaaaaattt
     1141 cccgcccgaa ccggtgttat ccggaggatg gtttggcaga aaagcgcaac aaaatgctca
     1201 ctatgtgggt gacagaagac gagcaccgcc gacttctgga gcgctgtgag ggtaaacaac
     1261 tcgcggcctg gatgcgccag atatgcctgg acgaaaagcc ctcgcgtgct ggcaaacttc
     1321 catccatctc gccggcgctg cttcgtcagc ttgccggcat gggtaacaac ctcaaccaga
     1381 ttgcccggca ggttaacgcc ggtggtggta ctgggcacga tcgcgtgcag gttgtcgccg
     1441 tgctgatggc cattgatgcc ggactcgagc ggctgcggca cgccgtgctg gaaaaggggg
     1501 cagacgatga tcgttaagtt tcatcccaga ggccgcggcg gtggcggcgg tccggtggat
     1561 tatctgctgg ggaaagaccg gcagcgcgac ggcgccagcg ttctgcaggg taagccggag
     1621 gaagtgcggg agcttattga cgcctcgcct tacgccaaga aatacacctc cggcgtgctg
     1681 tcttttgccg aacaggattt gccgcccggc cagcgtgaaa agctgatggc gagctttgag
     1741 cgggttctga tgcccggact cgataaagac cagtacagcg tactgtgggt tgagcaccgg
     1801 gacaaagggc ggctggagct gaacttcctg atcccgaaca cggagctgct gaccggcaga
     1861 cgtctccagc cgtattacga ccgcgccgac cgtccgcgca ttgatgcctg gcagaccata
     1921 gtgaacggca gactggggct gcacgacccg aacgcgccgg aaaaccggcg ggcgctggtt
     1981 acaccgtccg cgctgccgga agcgaagcag gaagccgccc aggcgattac gcgcggccta
     2041 ctttcccttg cctcatccgg ggagctgaaa acccgtcagg acgtcactga ggcgctggaa
     2101 agtgcgggtt ttgaggtggt gcgcaccacg aaaagcagca tcagcattgc cgaccctgac
     2161 ggggggcgaa acatccgact gaagggagcc atctatgaac agtcttttaa cgctggcgaa
     2221 ggacttagag cagaaatcga aagcgcagca gcagactacc ggcgagatgc tgaaagccgc
     2281 attcagcgag cacgagaagt ctgtcagagc ggaactgagc gaaagcgaga agagaatcag
     2341 cgccgccatc ctcgaccacg accggaagct gtcctcagcc atgagccaac gcacgaaagg
     2401 gatgctgcgt atgatcagcc agacgtggct gaccatagtc ctggtctccg cgctactgat
     2461 cgcctcgagc gcgggcattc tgtggtggca ggggcaacag atactcgaca actacacgac
     2521 catccaggaa cagaagagca cgcaggccat gctttcagag aagaacaacg gcgtccagct
     2581 cacgacctgc ggggaggaga gacgccgctg cgtgagggtg aacccggaag cgggaagatt
     2641 cggagaggat tcgagctgga tgatactggc ggggaaatag cacatgacgg aactggaaaa
     2701 acagttgctg agcgcattag agcagctaca gcaggactac tcgaaaaggc tggacgagtg
     2761 ggagaacgcc ttcgcggaat ggcggacgat gtctgggctt atgcaacggg agaacgcggc
     2821 gctgagcgag cgcgtcacgg gcttgagcag gcaggtgcag agtttgagcg atcagctgcg
     2881 ccgattgtcg caaggctgaa tggcatcgag gcgcaccggg agcaggagcg cgcggcgcag
     2941 caccagaaag cgctggagct ggaacgatcg cagcggcaga aaggttttga gcttggaatg
     3001 tagttaatca atgaaaaggg atgcgttatg aaatgtttct gggcttgctc agtctcggtg
     3061 gttttggcta tgtcatttac agtcgctgct gcggagaata acgacaacgt tacatataca
     3121 aaaccgtcag ccgggaggga cttatatctt acctgtaaag gttatcaggt gaagggggca
     3181 tctgtaatta acgtcgagaa accttcttac cttgaaggta ctggtgagca ggttgaattt
     3241 gcaatcatta ctcctgttgg tgcgtctgac ggactcaagg tcttttttga ttcatggggt
     3301 ttttcttcat ttggattgat tgaaagccat gtgatgcatg agcactggtc tttagttcat
     3361 gttggggggc gtgcttcagt caaaggtgaa aagattgatt attcatttgt agataaccag
     3421 ccacaggagg gggggagcta taaacccaaa acaggtgtgt tcctgtacgg ctgcatgaac
     3481 tcggataaaa gaccatcttg ggtcgaaaag atctacacaa gaacaggtgt gtttcgaggg
     3541 ggcatagaag actaaaatac tgcttacagc atgaaaatcc attgaacaga gtgtcagttc
     3601 atttccgtgc ataactatgc ataccgtaag aacttacggg gggcatttat cggcgttttt
     3661 acgtggtaag aggtgctctt ttgcggttca tggcgcagaa cggtgctgag gctgtctgcg
     3721 gcggtgcgaa caagggatgt tatggtaaat aagagtgtct tttggatatt ttaaatctgt
     3781 ttttttatta aatttaatgg gggcagaaaa tgggggattt tgagcgtacc tttggagctg
     3841 gtgctgattt tgatcggata attgatgaga ataacagcga atattttcga gaagatcgcc
     3901 gaaaaactaa aaattcaaaa aaaaaattct cttcttttca agatgctttg gtttgggcga
     3961 aagctaatcc tggcaaaacg ataataagat ctccagacgg tgtggggttt attgaaaa
//
