LOCUS       CP082413                3374 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain
            FSIS11704880 plasmid pF18S034-2, complete sequence.
ACCESSION   CP082413
VERSION     CP082413.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN08025063
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Derby
  ORGANISM  Salmonella enterica subsp. enterica serovar Derby
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3374)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3374)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3374)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Assembly Name                     :: F18S034
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 601x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 11:00:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,746
            CDSs (total)                      :: 4,628
            Genes (coding)                    :: 4,534
            CDSs (with protein)               :: 4,534
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 41 of 94
            Pseudo Genes (incomplete)         :: 53 of 94
            Pseudo Genes (internal stop)      :: 21 of 94
            Pseudo Genes (multiple problems)  :: 18 of 94
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..3374
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704880"
                     /serovar="Derby"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pF18S034-2"
                     /geo_loc_name="USA:IA"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            complement(9..242)
                     /locus_tag="CVB56_023700"
     CDS             complement(9..242)
                     /locus_tag="CVB56_023700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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="UAF25088.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(249..809)
                     /locus_tag="CVB56_023705"
     CDS             complement(249..809)
                     /locus_tag="CVB56_023705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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="UAF25089.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISGHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(778..1497)
                     /locus_tag="CVB56_023710"
                     /pseudo=""
     CDS             complement(778..1497)
                     /locus_tag="CVB56_023710"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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(1487..1810)
                     /locus_tag="CVB56_023715"
     CDS             complement(1487..1810)
                     /locus_tag="CVB56_023715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="UAF25090.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1874..2065
                     /locus_tag="CVB56_023720"
     CDS             1874..2065
                     /locus_tag="CVB56_023720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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="UAF25087.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2147..2227)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.585"
                     /coverage="93.0"
                     /evalue="4.04e-16"
     Typing          complement(2..1497)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.391"
                     /coverage="94.0"
                     /evalue="0.0"
ORIGIN
        1 ttcatccctt agctgttgtt cgcgataaat aaccgactca agcgatccac ttgcccggct
       61 aatctctgca cctgctgact caatatcacg acgcgctcgt tcagtatcgc gttgttccgt
      121 tgcgtaacct cgtgcatctt ctgcaattcc gcgaaggcgc tctcccactc gttcagccgc
      181 cgcatatagt cctgttgcaa atgctctaag gcgttcagca aatgcccttc cagttccgtc
      241 atactcgttt actccctgac cagcctcacg gcgttcttgt cgcccaccgt ccaggtgttt
      301 tcccctttca ccccgtccgg caacaccaga aatttcccgt tctcgccatt gacgaacgtc
      361 accccccagg tttttgcctc gagtttcgcc agcgtgtttt cctgctctct gatagtcagg
      421 atatttttcg caatcttgct ttcctgccac tccatcagcc cccagcaccc caggaaaatc
      481 ccgcccgtga cgctgagcgc ggtcagcgcc ggaaacagta tccgcccttt gatcacccgc
      541 cagagcagtt ttttctgctg ccgggacagt tcggcctctg tggtgctgaa ctgcatgctc
      601 acggtggtgc tcagcgtatc cagttgcttt ttcacggatg ttgtatgtcc gctgatagcg
      661 tctctgattt tctgcctgtt taagctcagt gccttgtcta cagactcttc gagcttcctg
      721 aactcgctgt tcagcatgtt ctcggtagaa gcggctcgct ctttcagttt cttctcgaag
      781 tctgttccca tttgtaaaag attgctcata cagcgccccc tttagcctga gattccgccc
      841 accctccggg tcggcaatac tgatactgct tctggttgtc ctcaccacct caaaacctgc
      901 cgctgtgagc gcctcagtga catcctgacg cgtttttatt gctccggcat ggtaaagcgc
      961 ctcaagaccc cgtgtaatcg cttctgcggc ctcctgtttc gcttttggca gattattcgg
     1021 tgtgacaagc gtccgtctgt tctccggtgc gttcgggtca cgcagcccgt aatgatgatt
     1081 aaccagcgtc tgccaggcat ttatcctcgg cctgtccgca cggtcgtagt acggctggag
     1141 gcgcttaccg ctctgtagct ccatgttcgg gatgacaaaa ttcagttcga gccgcccctt
     1201 atcctggtgt tccacccaaa gaatgctgta ctggtctttt tcgagaccgg gcataagaac
     1261 acgctcaaag ctcgtcatca ctctttcgcg ttcacccggc ggtaactcct tctccgcgaa
     1321 cgacagaacg cctgacgtgt atttcttcga aaatggcgtg gaatcaatga gttcccgcac
     1381 ttcttccggg ttaccccgga gcaccgttgc gccttcgcgg ttacgctccc gccccagcag
     1441 gtaatcgacc gggccacttc caccgccttt ccccctggca tgaaatttaa ctatcatccc
     1501 gtaccccctg ttccctgaca gcctgccgca actggcgcaa ttcaccctcg atggccatca
     1561 gtgcggccac cacatgaacc cggtcaatcg aagaccactg gccgctgttc accttccggg
     1621 ctgtctggtt caggttgttc ccgatggcag ccagatgccg cagcaatggc ggtgccagtg
     1681 tcggcagttt tcctgtgcgt gcaaccggct cccccagaca gacccgccgc atccattccg
     1741 ccagtcgttt accctcgcag cgttccagta accgggcgtg ctcctcatcg gtaacccgta
     1801 tcgtgagcat cttctcgcgt ttcatcggta tcattccccc taacaaatcc cccatacaag
     1861 gagccttaag accatgacca aacaggaaaa aacagccctt aacatggctc gctttatcag
     1921 aagccagacg ctaaccctgc tggaaaaact caacgatctg gacgcggacg aacaggcaga
     1981 catctgcgaa tcacttcacg accacgccga cgaactctac cgcagttgcc tcgcacgctt
     2041 cggcgatgac ggtgaaagca actgaaacat gcagctcccg gagacgttca cagcttgcct
     2101 gtgagcggat gccgggagca gacaagcccg ccagggcgcg tcagtgcggg tgtcggggcg
     2161 cagccctgac ccagttcaca gagcgatagc gatgtgtata ctggctttcc tcattttgca
     2221 tcggtgcaga gtggatggga agtgcaccat gtcaggagta aaaagccgca cagatgcgta
     2281 aaaacagcgc gcccgataaa caacacacac tcggacactg gcacaggcgc gtaagtgcac
     2341 aatgcttgcc tctgtgactc ttccgcttcc tcgcccactc gctcactacg ttcggtcgct
     2401 ggggctgcgg cgagcggtgg gatcactctc gttgtgatgc agatccgttt tttttttttg
     2461 cactggagtt atcaggagta gcggtgcaca tgggatcgtg cgatatgctg gatggtggaa
     2521 ggtcggaggg aacggcaaca actcacccct cccagtgaag ggacgggtag tttgccgctc
     2581 tcgatatgcc ggacggagcc aaggccatcg atcacggggc gcgtcagtgg aagaacccgc
     2641 gcctgcgtga cgtatgcgtc ttcgccgcac catctcaccc gtcacgccac cacataccgg
     2701 gaactgccgc caaggtctaa ctcaaccaat ctagccgcgc tacatacggt ttttgtggca
     2761 actcatcagg tgtccgctgt cgatgaaact ctctgcgccg gtagcggaac tctcacgcgt
     2821 gcggtcgccg tcgtcacagc tcccccaacc gcaaacgatt ctcgcaaata cgcaagtatc
     2881 tgcaaaaaca ggtttttttc ggggttcctg ggagactgtg ctgttgaaaa attcttgaag
     2941 aatacagaag gctcatgcaa actgaatgaa ctggtttctg ttgtggatct caacagtttc
     3001 cacaggaaca ttgaggaggt cagagacctc aatgaacccg aaacagctcg ccttcctggc
     3061 gagctgtttt cgttctacgc ccgccgacga aagatcgcaa gtgcaataac gagatttttc
     3121 acgtctttac gctcaaaaag taaaaaaacc atgttttccc ctggctgaat ccccaaaaac
     3181 gcgtgaaatg cgttttcagg atgttgcata gctatgcaca aatacggcac acgatttgtt
     3241 tcgctcgccc cagccgtcga acgggtcaaa atggcaagat ttcgtcactt ccccggtcac
     3301 atctccattg atggcccact ccgaacccgt gccgcgcgtt cctgtacctc atgtctgtac
     3361 cgggcacgct cctg
//
