LOCUS       CP082470                4681 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            FSIS1607455 plasmid pF18S013-3, complete sequence.
ACCESSION   CP082470
VERSION     CP082470.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05661217
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4681)
  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 4681)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4681)
  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                     :: F18S013
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 379x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:43:58
            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)                     :: 5,291
            CDSs (total)                      :: 5,168
            Genes (coding)                    :: 5,039
            CDSs (with protein)               :: 5,039
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 51 of 129
            Pseudo Genes (incomplete)         :: 78 of 129
            Pseudo Genes (internal stop)      :: 23 of 129
            Pseudo Genes (multiple problems)  :: 20 of 129
            CRISPR Arrays                     :: 3
            ##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..4681
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607455"
                     /serovar="Typhimurium"
                     /isolation_source="Animal-Turkey-Young Turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pF18S013-3"
                     /geo_loc_name="USA:VA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            138..725
                     /locus_tag="BGP52_026375"
     CDS             138..725
                     /locus_tag="BGP52_026375"
                     /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="UAE45977.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            complement(826..1131)
                     /locus_tag="BGP52_026380"
     CDS             complement(826..1131)
                     /locus_tag="BGP52_026380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015379333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="UAE45981.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1179..1448)
                     /locus_tag="BGP52_026385"
     CDS             complement(1179..1448)
                     /locus_tag="BGP52_026385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019080654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE45982.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            complement(1758..1940)
                     /locus_tag="BGP52_026390"
     CDS             complement(1758..1940)
                     /locus_tag="BGP52_026390"
                     /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="UAE45978.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            complement(2037..2246)
                     /locus_tag="BGP52_026395"
     CDS             complement(2037..2246)
                     /locus_tag="BGP52_026395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="UAE45979.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2250..2735)
                     /locus_tag="BGP52_026400"
     CDS             complement(2250..2735)
                     /locus_tag="BGP52_026400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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="UAE45980.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(2710..3423)
                     /locus_tag="BGP52_026405"
                     /pseudo=""
     CDS             complement(2710..3423)
                     /locus_tag="BGP52_026405"
                     /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(3413..3736)
                     /locus_tag="BGP52_026410"
     CDS             complement(3413..3736)
                     /locus_tag="BGP52_026410"
                     /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="UAE45983.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3846..4025)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          4005..4487
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.164"
                     /coverage="93.0"
                     /evalue="2.1e-176"
     Typing          complement(1928..3423)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcccacccga gaatctcaag aagatccttc aactctgtgt tcaaaacact gtttaaaaca
       61 gctataagcc ttcaagatag tttcagaaat acaatgctat ttcactctct ggaaaacaaa
      121 ccaaaaaggt caaaaaaatg ataagaaaga ttttttttgc ttctgcaatc gtaatagcca
      181 tctctggctg tacagcaatg gataaattgg caggaatggg tgttgtttct cagcaaacat
      241 caacctttga taactcgacc gttatagagg tatctccaaa ttcgctatac gatcctaaca
      301 gcacttgggg aacacaactt cagttgggcg cgatatggtc tagtgcctat ccagaagagg
      361 ttgggctaat tctttcctac aactcgaatg tatctagcgg aaatgccgca tacttaggtt
      421 tgacggggat tgatataaat attgatggca aaatatccag ctataaagca cagcagcaaa
      481 ctaatctaag cagtagcgca tataactccg tatctaaaac gatctatacc tctagcaaga
      541 acactgttgt tatcccctat aaattgctgg agagcatggt atcagctaaa aactgccgca
      601 ttcgcataca cacaagccaa ggaaatcaag acatcgactt ctcggcgcaa agcatccctg
      661 gaggtaaagc gacagcgatc gtttccatta aagagttcat ggtcaaagtc gaaagtttta
      721 aataaggaca cgtaagccca cctatatcta ctaacttagt gttaataggc ataggtggaa
      781 atttttgtct gcacgaaaaa acccgacgat gccgggtgtt tagtgttaat tcagcaaatt
      841 atagcgatac agctgctttt caaaatcctg cttcatgctc acaaacaaca gtatttcgat
      901 gttcgttccg tcaaaatcgt aaagcaccct gtattcactc tcaacatcga gccgctcacg
      961 taaaagcata cctcgatcct gtaagtggaa attgtagtga taacgttcag ggtcttggat
     1021 aatgcaggca actgattcct gaagtaagtt atcaaccaga tcaccggcct tgagtgaccc
     1081 aatgtatcca ctcttgtaag actcgatatc agctaaacat tgatatgcca tcggcgcgat
     1141 tgaaaccgtg tattgctggg acactaaaca cctctctgtt attttctagc ggcacgcaac
     1201 ctccctaaga cctcttctgg ggtcatgcct ttgccttctg tgatttcctt tttagccaac
     1261 gttgccagct taaaaagggc gttgatattg cgttcttctc tcatctcacg aacttcagca
     1321 tcacgttctg ctgcggtttg gatgaataac tcagctactc cgtttttagt gacgtaaaca
     1381 cctccttcaa aggtttgtgc atttccgaga ctgtctcttg cgagtttctg ggacatggtc
     1441 tggttcatag gcattttttt ctcatcatat aggggcgctt ccggcgagaa cggcgctgca
     1501 cgattcaagg gtcatagttt ccggtttgtg gtttcaggtt tcaggtttca ggtttcaggt
     1561 ttcagtgttg atttattagg ccagtacaaa ttctcgctat ggcacatggt ggccagtgtc
     1621 cgtgctttga atagagttta tcagttggtg tataaattga gtacatattt ttacacagaa
     1681 aggtgaaaga agggaaaatt agtttaattc agaatcattt accataacat ctcttaccgg
     1741 caccgctccg gacgggttca gcgcgaatgc gccgtcagcc cggaaaaaaa tacagttaac
     1801 tccccggtaa aacgcgccgc ctgcgcctga taaatttcac ccgaatgcat agccatgcag
     1861 acaggtgaat ggcaccggct ttcgccgcag atattcgccg aaagccccgt tttatccggt
     1921 ttgttacagc gacggtccat tgtacgtccg ctgccgctgc gatcgttcaa gctccagcgt
     1981 tttctggtgc tgcaccgccc gctcatgctc ccggtgtgct tcaatgccgt ctagtctcac
     2041 gacaaccggc gaagctgctc gctcaaactc tgcacctgcc tgctcaagcc cgtgacgcgc
     2101 tcgctcagcg ccgcgttctc ccgttgcata agaccagaca tcgtccgcca ttccgcgaag
     2161 gcgttctccc actcgtccag ccttttcgag tagtcctgct gtagctgctc taatgcgctc
     2221 agcagctgtt tttccagctc cgtcatgtgc tatttccccg ccagtatcat ccagctcgaa
     2281 tcctctccga acccgcccgc ttccgggttc accctcacgc agcggcgtct ctgctctccg
     2341 caggtcgtga gctgcacacc gctgttcctc tctgacagca tggcctgcgt gttcttctgc
     2401 tcccggatgg tcgtgtagtt ctcgagtatc tgctgcccct gccaccacag aatgcccgcg
     2461 ctcgaggcga tcagcagcgc ggagaccagc acgatggtca gccacgtctg gctgaccatg
     2521 cgcagcatcc ctttcgtgcg ctggctcatg gctgaggaca gcttccggtc gtggtcgagg
     2581 atggcggcgc tgattctctt ctcgctttcg ctcagttccg ctctgacaga cttctcgtgc
     2641 tcgctgaatg cggctttcag catctcgccg gtagtctgct gctgcgcttt cgatttctgc
     2701 tctaagtcct tcgccagcgt taaaagactg ttcatagatg gctcccttca gtcggatgtt
     2761 tcgccccccg tccgggtcgg caatgctgat gctgcttttt gtggtgcgca ccacctcaaa
     2821 acctgcgttt tccagcgcct cagtgacgtc ctgtcgcgtt ttcagctccc cggacgaggc
     2881 taaggccagt aaaccccgcg taatagtctg ggcagcttcc tgcttcgttt ccggcagcgc
     2941 ggacggcgtg gccagcgccc gccggttctc cggcgcgttc gggtcgtgca gccccagccg
     3001 accgttcacg atggtctgcc aggcatcgat gcgcggacgg tcggcgcggt cgtaatacgg
     3061 ctggagacgc ctgccggtca gcagctccgt gtttggtatc aggaaattca gctcaagccg
     3121 ccctttgtcg ttgtgctcaa cccacagcac gctgtactga tctttatcga gtccgggcat
     3181 cagaacccgc tcgaagctcg ccatcagctt ttcacgctgt ccgggcggta agtcctgttc
     3241 ggcaaatgac aggacgccgg aggtgtactt tttggcgtaa ggcgaggcat cgataagctc
     3301 ccggacttcc tccggcttcc cctgcagaac gctggcgccg tcgcggtgcc ggtctttgcc
     3361 cagcagataa tccaccggac cggcaccgcc gccgcgccct ctcgggtgaa acttaacgat
     3421 catcgtctgc ccctttttcc agtacggcgt gccgcagccg ctcgagtcct gcgtcgatgg
     3481 ccatcagcgc agcgacaacc tgcacgcggt cgtgcccgct gccgccaccg gcgttaacct
     3541 gccgggcaat ctggttgagg ttgtttccca tgccggcaag ctgacgaagc agcgccggcg
     3601 agatcgaggg aagtttgccg gcgcgggcgg gcttctcgtc caggcacgtc tggcgcatcc
     3661 aggccgcgag ctgtttaccc tcgcagcgct ccagcagacg cctgtgctca tcttccgtca
     3721 cccacatcgt gagcattttg ctgcgtttat ctgccaatcc ggcctcctga taacgccggg
     3781 acgggcggga aattctttcc cgggcggcgc ggtgttgggc aagccgcagg cgcgtcagtg
     3841 gcttttagcg ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat
     3901 actggcttaa tatagtaaat cgaagtggga attcagggaa gtgcttcatg tgacagagga
     3961 aaaatgcggc tgtggggcgt aagtgcagaa tgtaggtaaa agtgaaatga cgcctcctcg
     4021 ctcactcggt cgctgcgctc ctgccgtgag actgcggcgg gcgttacagg ctcacggata
     4081 acgagataaa gcggaaggcg acacatcaga aaggaacaga aaaaggatgc ggcgttgccg
     4141 tttttccata ggctccgccc ccctgacgag catcacgaaa tctgacgctc aaatcagtgg
     4201 cggcgaaacc cgacaggact ataaagatcc caggcgtttc cccctggtag ctccctcatg
     4261 cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcggttt
     4321 ctcattccac gcctgacact cagttccggg taggcagttc gctccaagct ggactgtatg
     4381 cacgaacccc ccgttcagtc cgaccgctgc gccttatccg gtaactatca tcttgagtcc
     4441 aacccggaaa gacacgactt atcgccactg gcagcagcca ttggtaagag gatgtacaag
     4501 agattactaa cgcagagttc ttgaagtatc agcccaacta cggctaaact ggaaggacga
     4561 atttggtggc agcggtcttg tacaccctgt taccacggtt cagaagttcc ccaacttact
     4621 gaaccatcga aaaaccacct ccccaggtgg ttttttcgtt tctgggtcaa gagattacga
     4681 c
//
