LOCUS       NZ_CP038606             4018 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg strain
            CFIAFB20170120 plasmid pGTAFD2016-MI-0253.2, complete sequence.
ACCESSION   NZ_CP038606
VERSION     NZ_CP038606.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10501887
            Assembly: GCF_004768625.1
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  JOURNAL   Unpublished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 (01-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 Name                   :: GCF_004768625.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 01:19:06
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,097
            CDSs (total)                      :: 4,977
            Genes (coding)                    :: 4,795
            CDSs (with protein)               :: 4,795
            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)              :: 182
            CDSs (without protein)            :: 182
            Pseudo Genes (ambiguous residues) :: 0 of 182
            Pseudo Genes (frameshifted)       :: 51 of 182
            Pseudo Genes (incomplete)         :: 144 of 182
            Pseudo Genes (internal stop)      :: 26 of 182
            Pseudo Genes (multiple problems)  :: 32 of 182
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP038606.1.
            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="CFIAFB20170120"
                     /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            complement(join(2960..4018,1..438))
                     /locus_tag="EIP71_RS26710"
                     /old_locus_tag="EIP71_26030"
     CDS             complement(join(2960..4018,1..438))
                     /locus_tag="EIP71_RS26710"
                     /old_locus_tag="EIP71_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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_034169352.1"
                     /translation="MIVKFHPRGRGGGGGPVDYLLGKDRQRDGASVLQGKPEEVRELID
                     ASPYAKKYTSGVLSFAEQDLPPGQREKLMASFERVLMPGLDKDQYSVLWVEHRDKGRLE
                     LNFLIPNTELLTGRRLQPYYDRADRPRIDAWQTIVNGRLGLHDPNAPENRRALVTPSAL
                     PEAKQEAAQAITRGLLSLASSGELKTRQDVTEALESAGFEVVRTTKSSISIADPDGGRN
                     IRLKGAIYEQSFNAGEGLRAEIESAAADYRRDAESRIQRAREVCQSGTERKREENQRRH
                     PRPRPEAVLSHEPTHERDAAYDQPDVADHSPGLRATDRLERGHSVVAGATDTRQLHDHP
                     GTEEHAGHAFREEQRRPAHDLRGGETPLREGEPGSGKIRRGFELDDTGGEIAHDGTGKT
                     VAERIRAATAGLLEKAGRVGERLRGMADDVWAYATGERGAERARHGLEQAGAEFERSAA
                     PIVARLNGIEAHREQERAAQHQKALELERSQRQKGFELGM"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(428..751)
                     /locus_tag="EIP71_RS26035"
                     /old_locus_tag="EIP71_26035"
     CDS             complement(428..751)
                     /locus_tag="EIP71_RS26035"
                     /old_locus_tag="EIP71_26035"
                     /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            1399..1512
                     /locus_tag="EIP71_RS26965"
                     /old_locus_tag="EIP71_26045"
     CDS             1399..1512
                     /locus_tag="EIP71_RS26965"
                     /old_locus_tag="EIP71_26045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072035093.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(1941..2153)
                     /locus_tag="EIP71_RS26050"
                     /old_locus_tag="EIP71_26050"
     CDS             complement(1941..2153)
                     /locus_tag="EIP71_RS26050"
                     /old_locus_tag="EIP71_26050"
                     /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            complement(2408..2935)
                     /locus_tag="EIP71_RS26055"
                     /old_locus_tag="EIP71_26055"
     CDS             complement(2408..2935)
                     /locus_tag="EIP71_RS26055"
                     /old_locus_tag="EIP71_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          complement(865..1042)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          989..1512
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.434"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2..438)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.26"
                     /coverage="99.0"
                     /evalue="2.97e-88"
     Typing          complement(2973..4018)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.1"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtgcagcccc agtctgccgt tcactatggt ctgccaggca tcaatgcgcg gacggtcggc
       61 gcggtcgtaa tacggctgga gacgtctgcc ggtcagcagc tccgtgttcg ggatcaggaa
      121 gttcagctcc agccgccctt tgtcccggtg ctcaacccac agtacgctgt actggtcttt
      181 atcgagtccg ggcatcagaa cccgctcaaa gctcgccatc agcttttcac gctggccggg
      241 cggcaaatcc tgttcggcaa aagacagcac gccggaggtg tatttcttgg cgtaaggcga
      301 ggcgtcaata agctcccgca cttcctccgg cttaccctgc agaacgctgg cgccgtcgcg
      361 ctgccggtct ttccccagca gataatccac cggaccgccg ccaccgccgc ggcctctggg
      421 atgaaactta acgatcatcg tctgccccct tttccagcac ggcgtgccgc agccgctcga
      481 gtccggcatc aatggccatc agcacggcga caacctgcac gcgatcgtgc ccagtaccac
      541 caccggcgtt aacctgccgg gcaatctggt tgaggttgtt acccatgccg gcaagctgac
      601 gaagcagcgc cggcgagatg gatggaagtt tgccagcacg cgagggcttt tcgtccaggc
      661 atatctggcg catccaggcc gcgagttgtt taccctcaca gcgctccaga agtcggcggt
      721 gctcgtcttc tgtcacccac atagtgagca ttttgttgcg cttttctgcc aaaccatcct
      781 ccggataaca ccggttcggg cgggaaattt tttcctgtcc ggagcggtgt tgggcaagcc
      841 cgcagggcgc ggcagtactt ttcagcgggt ttcggggcgc agccctgaac cagtcacgta
      901 gcgctagcgg agtgtatact ggcttaacat ggtaaatcgg agtggggatt caggaaagtg
      961 cttcatgtgg cagggagaaa atgctgctgt ggggcgtaag tgcgaaatgc agatcccggt
     1021 gaaatgacgc ctcctcgctc actcggtcgc tgcgctcctg ccgtgagact gcggcgggcg
     1081 ttgccagctt acgaatggct ggataaagag actaagcgga aatcaatcag aaagggcgga
     1141 aaaaggatgc ggcgttgccg tttttccata ggctccgccc ccctgacaag catcacgaaa
     1201 tctgacgctc aaatcagtgg tggcgaaacc cgacaggact ataaagatcc caggcgtttc
     1261 cccctggtag ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc
     1321 cgctgttatg gccgcgttta tctaattcca cgcctgacac tcagttccgg gtaggcagtt
     1381 cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgaccgctg cgccttatcc
     1441 ggtaactatc gacttgagtc caacccggaa agacacgaca aaacgccact ggcagcagcc
     1501 actggtaact gatttagagg agttagtctt gaagttatgc gccggttaag gctaaactga
     1561 aaggacaagt tttggtgact gtgctcctcc aagccagtta cctcggttca aagagttgct
     1621 gctctgagaa ccttcgaaaa aaccgccttg ctgggcggtt ttttcgttta cagtgctaag
     1681 agattacgat tctccatgaa tgatctcaag aagatccgtt taaaaaagcg ggttttatgg
     1741 ggggataaag ttcgtctagc ccagtcactt tggattacag ctaggtttcg taagccatgc
     1801 aagaatgcct gtaactaaca aaataggccc tgcaacgtac gtaacataga ctccaacata
     1861 cgacactgtg aaacatatga gtacgtatat agacagtgtt gtccaaaaaa tgactgttgt
     1921 tttacagtga atccactctt tcatttttca ataaacccca caccgtctgg agatcttatt
     1981 atcgttttgc caggattagc tttcgcccaa accaaagcat cttgaaaaga agagaatttt
     2041 ttttttgaat ttttagtttt tcggcgatct tctcgaaaat attcgctgtt attctcatca
     2101 attatccgat caaaatcagc accagctcca aaggtacgct caaaatcccc cattttctgc
     2161 ccccattaaa tttaataaaa aaacagattt aaaatatcca aaagacactc ttatttacca
     2221 taacatccct tgttcgcacc gccgcagaca gcctcagcac cgttctgcgc catgaaccgc
     2281 aaaagagcac ctcttaccac gtaaaaacgc cgataaatgc cccccgtaag ttcttacggt
     2341 atgcatagtt atgcacggaa atgaactgac actctgttca atggattttc atgctgtaag
     2401 cagtatttta gtcttctatg ccccctcgaa acacacctgt tcttgtgtag atcttttcga
     2461 cccaagatgg tcttttatcc gagttcatgc agccgtacag gaacacacct gttttgggtt
     2521 tatagctccc cccctcctgt ggctggttat ctacaaatga ataatcaatc ttttcacctt
     2581 tgactgaagc acgcccccca acatgaacta aagaccagtg ctcatgcatc acatggcttt
     2641 caatcaatcc aaatgaagaa aaaccccatg aatcaaaaaa gaccttgagt ccgtcagacg
     2701 caccaacagg agtaatgatt gcaaattcaa cctgctcacc agtaccttca aggtaagaag
     2761 gtttctcgac gttaattaca gatgccccct tcacctgata acctttacag gtaagatata
     2821 agtccctccc ggctgacggt tttgtatatg taacgttgtc gttattctcc gcagcagcga
     2881 ctgtaaatga catagccaaa accaccgaga ctgagcaagc ccagaaacat ttcataacgc
     2941 atcccttttc attgattaac tacattccaa gctcaaaacc tttctgccgc tgcgatcgtt
     3001 ccagctccag cgctttctgg tgctgcgccg cgcgctcctg ctcccggtgc gcctcgatgc
     3061 cattcagcct tgcgacaatc ggcgcagctg atcgctcaaa ctctgcacct gcctgctcaa
     3121 gcccgtgacg cgctcgctca gcgccgcgtt ctcccgttgc ataagcccag acatcgtccg
     3181 ccattccgcg aaggcgttct cccactcgtc cagccttttc gagtagtcct gctgtagctg
     3241 ctctaatgcg ctcagcaact gtttttccag ttccgtcatg tgctatttcc ccgccagtat
     3301 catccagctc gaatcctctc cgaatcttcc cgcttccggg ttcaccctca cgcagcggcg
     3361 tctctcctcc ccgcaggtcg tgagctggac gccgttgttc ttctctgaaa gcatggcctg
     3421 cgtgctcttc tgttcctgga tggtcgtgta gttgtcgagt atctgttgcc cctgccacca
     3481 cagaatgccc gcgctcgagg cgatcagtag cgcggagacc aggactatgg tcagccacgt
     3541 ctggctgatc atacgcagca tccctttcgt gcgttggctc atggctgagg acagcttccg
     3601 gtcgtggtcg aggatggcgg cgctgattct cttctcgctt tcgctcagtt ccgctctgac
     3661 agacttctcg tgctcgctga atgcggcttt cagcatctcg ccggtagtct gctgctgcgc
     3721 tttcgatttc tgctctaagt ccttcgccag cgttaaaaga ctgttcatag atggctccct
     3781 tcagtcggat gtttcgcccc ccgtcagggt cggcaatgct gatgctgctt ttcgtggtgc
     3841 gcaccacctc aaaacccgca ctttccagcg cctcagtgac gtcctgacgg gttttcagct
     3901 ccccggatga ggcaagggaa agtaggccgc gcgtaatcgc ctgggcggct tcctgcttcg
     3961 cttccggcag cgcggacggt gtaaccagcg cccgccggtt ttccggcgcg ttcgggtc
//
