LOCUS       NZ_CP039274             4096 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg str.
            CFSAN004025 plasmid pCFSAN004025.4, complete sequence.
ACCESSION   NZ_CP039274
VERSION     NZ_CP039274.1
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 4096)
  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  JOURNAL   Unpublished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 4096)
  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
            CP039274.1.
            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..4096
                     /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="pCFSAN004025.4"
                     /geo_loc_name="Mexico"
                     /collection_date="2003-07-03"
                     /collected_by="FDA"
     gene            join(3976..4096,1..107)
                     /locus_tag="CFSAN004025_RS26140"
                     /old_locus_tag="CFSAN004025_26445"
     CDS             join(3976..4096,1..107)
                     /locus_tag="CFSAN004025_RS26140"
                     /old_locus_tag="CFSAN004025_26445"
                     /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(637..846)
                     /locus_tag="CFSAN004025_RS26145"
     CDS             complement(637..846)
                     /locus_tag="CFSAN004025_RS26145"
                     /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(850..1335)
                     /locus_tag="CFSAN004025_RS26150"
     CDS             complement(850..1335)
                     /locus_tag="CFSAN004025_RS26150"
                     /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            complement(<1370..2074)
                     /locus_tag="CFSAN004025_RS26155"
                     /pseudo=""
     CDS             complement(<1370..2074)
                     /locus_tag="CFSAN004025_RS26155"
                     /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            complement(2013..2336)
                     /locus_tag="CFSAN004025_RS26160"
                     /old_locus_tag="CFSAN004025_26455"
     CDS             complement(2013..2336)
                     /locus_tag="CFSAN004025_RS26160"
                     /old_locus_tag="CFSAN004025_26455"
                     /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            2975..3133
                     /locus_tag="CFSAN004025_RS26880"
                     /old_locus_tag="CFSAN004025_26465"
     CDS             2975..3133
                     /locus_tag="CFSAN004025_RS26880"
                     /old_locus_tag="CFSAN004025_26465"
                     /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="hypothetical protein"
                     /protein_id="WP_032670878.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHEKSLLAAAISNWRYTRDKL
                     RGLEVWA"
                     /name="hypothetical protein"
     gene            complement(3370..3639)
                     /locus_tag="CFSAN004025_RS26175"
                     /old_locus_tag="CFSAN004025_26470"
     CDS             complement(3370..3639)
                     /locus_tag="CFSAN004025_RS26175"
                     /old_locus_tag="CFSAN004025_26470"
                     /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            3721..3954
                     /locus_tag="CFSAN004025_RS26180"
                     /old_locus_tag="CFSAN004025_26475"
     CDS             3721..3954
                     /locus_tag="CFSAN004025_RS26180"
                     /old_locus_tag="CFSAN004025_26475"
                     /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"
     Typing          complement(2445..2523)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.8899999999999995e-34"
     Typing          2599..3087
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.747"
                     /coverage="94.0"
                     /evalue="7.82e-151"
     Typing          complement(528..2023)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.998"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcctacaga atcagactca ggcctgctgg gctataaaga cgcaaatggt gtcaaacagc
       61 agatcaataa agccgacgtt aaagaagtct ctgaaattcc gcattgaggc atcgctctct
      121 ccgaaaaggg ccgctaatgc ggcccttttc tttatctgcc ccaacaacag gcaaaaaaag
      181 cccccgctgg gggccaaata cctgcagtgg ctggatagta ctgcattcct gatgaaggag
      241 acgaataagt atgggccgga tttttgcgtc tgcaggctcg gtcgccacaa tttttccgta
      301 cccgccaggc atcatgcttt taccataaca tcccttgccc gcacctctcc ggacgggttc
      361 agcgcgaatg cggcgtcagt cctgcaaaac cgacagtaaa ccaccccgca aaccgtgcat
      421 tctgcgcctg ataaatctca cccgactgca tagccatgca gccgggtgaa tggcaccggg
      481 tttcggcgca gatcctcaat gaaagccccg ttttatccgg ttatcacagc gacggaccgt
      541 catactcctg ctgacgctgc gatcgttcca gctccagcgc tttctggtgc tgcgctgcgc
      601 gctcctgctc ccggtgtgcc tcgatgtcgt tcagccttac gacaaccggc gcagctgctc
      661 gcttaaactc agcacctgcg tgctcaagtc cgtgacgcgc tcgctcagcg ctgcgttctc
      721 ccgttgcata agaccacaca tcgtccgcca ttccgcgaag gcgctctccc actcgtccag
      781 ccttttcgag tagtcctgct gtagctgctc taatgcgctc agcaactgtt tttccagttc
      841 cgtcatgtgc tatttccccg ccagtatcat ccagctcgaa tcctctccga accgtcccgc
      901 gtccgggttc accctcacgc agcggcgtcg ttcctctccg caggtcgtga gctgcacgcc
      961 gctgttcctc tcggacagca tggcctgcgt gctcttctgc tcccggatgg tcgtgtaatt
     1021 gtcgagtatc tgctgcccct gccaccatag aatgcccgca cttgaggcta tcagcagcac
     1081 ggagaccagg acgatggtca gccacgtctg gctgaccatg cgcagcatcc ctttcgtacg
     1141 ctggctcatg gctgaggaca gcatccggtc gtggtcgtgg atggcggcgc tgattctctt
     1201 ctcgctttcg ttcagttccg ctctgacaga cttctcgtgc tcgctgaatg cggctttcag
     1261 catctcgccg gtagtctgct gctgcacttt cgatttctgc tctaagtcct tcgccagcgt
     1321 taaaagactg ttcatagatg gctcccttca gtcggatgtt tcgccccccg tccgggtcgg
     1381 caatgctgat gctgcttttt gtggtgcgaa ccacctcaaa acctgcgctt tccagcgcct
     1441 cagtgacgtc ctgacgcgtt ttcagctccc cggacgaggc taaggccagt aaaccccgcg
     1501 taatcgcctg agcggcttcc tgcttcgttt ccggcagcgc ggacggcgtg accagtgccc
     1561 gccggttttc cggcgcgttc gggtcgtgca gccccagact gccgttcacg atggtctgcc
     1621 aggcatcaat gcgaggacgg tcggcgcggt catagtatgg ctggagccgt ttgccggtca
     1681 gcagctccgt gttcgggatc aggaagttca gctccagccg ccccttgtcc cggtgctcaa
     1741 cccacagcac gctgtactgg tctttatcga gtccgggcat cagaacccgc tcgaagctcg
     1801 ccatcagcgt ttcacgctgc ccgggcggta agtcctgttc ggcaaaggac agcaccccgg
     1861 aggtgtactt tttggcgtag ggcgaggcgt cgataagctc ccggacttcc tccggcttcc
     1921 cctgaagaac gctggcaccg tcgcgctggc ggtctttccc cagcagataa tcaaccgggc
     1981 cggcaccgcc tccgcgtccc cggggatgaa acttaacgat catcgtcagc ccccttttcc
     2041 agtacggcat gccgcagccg ctcgagtccg gcatcgatgg ccatcagcgc ggcgacgacc
     2101 tgcacgcggt cgagaccgct actgccaccg gcgttaacct ggcgggcaat ctggttgagg
     2161 ttgttcccca tgccggcaag ctgacgaagc agcgccggcg agatcgaggg aagtttgccg
     2221 gcccgggcgg gcttctcgtc caggcacgtc tgccgcatcc aggccgcgag ctgtttaccg
     2281 tcgcagcgtt ccagcagacg gcggtgctca tcttctgtta cccacatcgt gagcattttg
     2341 ctgcgtttgt ctgccaatcc ggcctcctga taacgccggg acgggcggga aatcttttcc
     2401 cggtcggcgc ggtgttgggc aagccgcagg cgcgtcagtg gcatttagcg ggtttcgggg
     2461 cgcagccctg aaccagtcac gtagcgctag cggagtgtat actggcttac tatggtggca
     2521 cgacgggaat cgggatgaaa tagtcagtca tgaaaactgt gagatgaggc tcaggtgcgt
     2581 aagaggctga tgcctgtccc ggtggatatt ccgcttcctc gctcactgac tcgctacgct
     2641 cggtcgttcg gctgcggcga gcggtacgga ctcacggata aagacgtggc ggggaaatac
     2701 gtgaatgcag gaggggaaga aaggatgcgc cgctgccggt tttccatagg ctccgccccc
     2761 ctgacaagca tcacagaatc tgacgctcaa atcagtggtg gcgaaacccg atgcggctta
     2821 aagataccag gcgtttcccc ctgatggctc cctcgtgctc ccccgcattc ctgcctttcg
     2881 gtttaccggt gtcattccgc tgttatggcc gcggtttctc attccacgcc tgacactcag
     2941 ttccgcgaag gcagttcgct ccaggattga ctgtatgcac gaaccccccg ttcagtccga
     3001 ctgctgcgcc ttatccggta actatcgtct tgagtccaac ccggaaagac acgaaaaatc
     3061 gctactggca gcagccatta gtaactggag gtatacgaga gacaaattaa gaggtcttga
     3121 agtatgggcc tgagagaggc tacactgaaa gaacagtttt ggtttctgcg gtctcgtata
     3181 cccagttacc tggttaagca gttccccaac tgacttaacc ttcgatcaaa ccacctcccc
     3241 aggtggtttt ttcgttttca gagcaagaga ttacgactgt aacgacagga tcacaagaag
     3301 atcatttact cagagagact aactaccact atgtttgcct atcaacatac ttaggaaaca
     3361 ttacttgagt taacgactcc accttacttt tagtatctcg caatgaatct tccgaccgcc
     3421 gttgtgttga agttctattg cgccaccggg gtataaatca ctttcgttta actcaattaa
     3481 aagctcgttc ttgtgagcat cctctaaata aaggtaataa cacccaccat aaaggttctg
     3541 cgtatctggc acggcaacaa aagatttctt tccgaacagt aaaacagcct ctttttctcc
     3601 atgctctgtc agcaataatc gaaattcttg tccattcaat cctcttttcg catgaaaaaa
     3661 cgacctatac ttagatggtt agtgaccata tccactttac ctttaagcag ggaacctatt
     3721 atgaataaaa aaacgctgtt ggcggccatg atggtcgcgt tggtgacctt tgccgctgct
     3781 ggatgttctt caaaccaaga aataaaaacc acagatgatc gcactatcgt tacagacggc
     3841 aaacccaaag ttgacagtga tacgggatta gtatcctaca aagatgccca tacaggccga
     3901 accgaacaga tcaaccgtga caaaattacc aacatgagtg aactagacaa ctgatacgga
     3961 taaaaggagc tggctttgaa aaagattttt gtttcagtgt tcgcagcggc agttgcgctt
     4021 tcagccctaa ccggctgcac gcgcacaagc tatgccatcc acaccaacga cgggcgtaca
     4081 attgtcagcg acggca
//
