LOCUS       CP082597                4674 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0666 plasmid pN18S0666, complete sequence.
ACCESSION   CP082597
VERSION     CP082597.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN11968060
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 4674)
  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 4674)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4674)
  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
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 363x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:18:45
            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)                     :: 4,861
            CDSs (total)                      :: 4,739
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 101
            CDSs (without protein)            :: 101
            Pseudo Genes (ambiguous residues) :: 0 of 101
            Pseudo Genes (frameshifted)       :: 32 of 101
            Pseudo Genes (incomplete)         :: 66 of 101
            Pseudo Genes (internal stop)      :: 21 of 101
            Pseudo Genes (multiple problems)  :: 15 of 101
            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..4674
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S0666"
                     /serovar="Typhimurium"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S0666"
                     /geo_loc_name="USA:SC"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(join(4627..4674,1..135))
                     /locus_tag="FH349_024270"
     CDS             complement(join(4627..4674,1..135))
                     /locus_tag="FH349_024270"
                     /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="UAH83487.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            complement(232..441)
                     /locus_tag="FH349_024275"
     CDS             complement(232..441)
                     /locus_tag="FH349_024275"
                     /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="UAH83488.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(445..930)
                     /locus_tag="FH349_024280"
     CDS             complement(445..930)
                     /locus_tag="FH349_024280"
                     /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="UAH83489.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(905..1618)
                     /locus_tag="FH349_024285"
                     /pseudo=""
     CDS             complement(905..1618)
                     /locus_tag="FH349_024285"
                     /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(1608..1931)
                     /locus_tag="FH349_024290"
     CDS             complement(1608..1931)
                     /locus_tag="FH349_024290"
                     /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="UAH83490.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3014..3601
                     /locus_tag="FH349_024295"
     CDS             3014..3601
                     /locus_tag="FH349_024295"
                     /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="UAH83486.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            complement(3702..4007)
                     /locus_tag="FH349_024300"
     CDS             complement(3702..4007)
                     /locus_tag="FH349_024300"
                     /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="UAH83491.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(4055..4324)
                     /locus_tag="FH349_024305"
     CDS             complement(4055..4324)
                     /locus_tag="FH349_024305"
                     /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="UAH83492.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     Typing          complement(2041..2220)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          2200..2682
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.164"
                     /coverage="93.0"
                     /evalue="2.1e-176"
     Typing          complement(123..1618)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggtaaaacgc gccgcctgcg cctgataaat ttcacccgaa tgcatagcca tgcagacagg
       61 tgaatggcac cggctttcgc cgcagatatt cgccgaaagc cccgttttat ccggtttgtt
      121 acagcgacgg tccattgtac gtccgctgcc gctgcgatcg ttcaagctcc agcgttttct
      181 ggtgctgcac cgcccgctca tgctcccggt gtgcttcaat gccgtctagt ctcacgacaa
      241 ccggcgaagc tgctcgctca aactctgcac ctgcctgctc aagcccgtga cgcgctcgct
      301 cagcgccgcg ttctcccgtt gcataagacc agacatcgtc cgccattccg cgaaggcgtt
      361 ctcccactcg tccagccttt tcgagtagtc ctgctgtagc tgctctaatg cgctcagcag
      421 ctgtttttcc agctccgtca tgtgctattt ccccgccagt atcatccagc tcgaatcctc
      481 tccgaacccg cccgcttccg ggttcaccct cacgcagcgg cgtctctgct ctccgcaggt
      541 cgtgagctgc acaccgctgt tcctctctga cagcatggcc tgcgtgttct tctgctcccg
      601 gatggtcgtg tagttctcga gtatctgctg cccctgccac cacagaatgc ccgcgctcga
      661 ggcgatcagc agcgcggaga ccagcacgat ggtcagccac gtctggctga ccatgcgcag
      721 catccctttc gtgcgctggc tcatggctga ggacagcttc cggtcgtggt cgaggatggc
      781 ggcgctgatt ctcttctcgc tttcgctcag ttccgctctg acagacttct cgtgctcgct
      841 gaatgcggct ttcagcatct cgccggtagt ctgctgctgc gctttcgatt tctgctctaa
      901 gtccttcgcc agcgttaaaa gactgttcat agatggctcc cttcagtcgg atgtttcgcc
      961 ccccgtccgg gtcggcaatg ctgatgctgc tttttgtggt gcgcaccacc tcaaaacctg
     1021 cgttttccag cgcctcagtg acgtcctgtc gcgttttcag ctccccggac gaggctaagg
     1081 ccagtaaacc ccgcgtaata gtctgggcag cttcctgctt cgtttccggc agcgcggacg
     1141 gcgtggccag cgcccgccgg ttctccggcg cgttcgggtc gtgcagcccc agccgaccgt
     1201 tcacgatggt ctgccaggca tcgatgcgcg gacggtcggc gcggtcgtaa tacggctgga
     1261 gacgcctgcc ggtcagcagc tccgtgtttg gtatcaggaa attcagctca agccgccctt
     1321 tgtcgttgtg ctcaacccac agcacgctgt actgatcttt atcgagtccg ggcatcagaa
     1381 cccgctcgaa gctcgccatc agcttttcac gctgtccggg cggtaagtcc tgttcggcaa
     1441 atgacaggac gccggaggtg tactttttgg cgtaaggcga ggcatcgata agctcccgga
     1501 cttcctccgg cttcccctgc agaacgctgg cgccgtcgcg gtgccggtct ttgcccagca
     1561 gataatccac cggaccggca ccgccgccgc gccctctcgg gtgaaactta acgatcatcg
     1621 tctgcccctt tttccagtac ggcgtgccgc agccgctcga gtcctgcgtc gatggccatc
     1681 agcgcagcga caacctgcac gcggtcgtgc ccgctgccgc caccggcgtt aacctgccgg
     1741 gcaatctggt tgaggttgtt tcccatgccg gcaagctgac gaagcagcgc cggcgagatc
     1801 gagggaagtt tgccggcgcg ggcgggcttc tcgtccaggc acgtctggcg catccaggcc
     1861 gcgagctgtt taccctcgca gcgctccagc agacgcctgt gctcatcttc cgtcacccac
     1921 atcgtgagca ttttgctgcg tttatctgcc aatccggcct cctgataacg ccgggacggg
     1981 cgggaaattc tttcccgggc ggcgcggtgt tgggcaagcc gcaggcgcgt cagtggcttt
     2041 tagcgggttt cggggcgcag ccctgaacca gtcacgtagc gctagcggag tgtatactgg
     2101 cttaatatag taaatcgaag tgggaattca gggaagtgct tcatgtgaca gaggaaaaat
     2161 gcggctgtgg ggcgtaagtg cagaatgtag gtaaaagtga aatgacgcct cctcgctcac
     2221 tcggtcgctg cgctcctgcc gtgagactgc ggcgggcgtt acaggctcac ggataacgag
     2281 ataaagcgga aggcgacaca tcagaaagga acagaaaaag gatgcggcgt tgccgttttt
     2341 ccataggctc cgcccccctg acgagcatca cgaaatctga cgctcaaatc agtggcggcg
     2401 aaacccgaca ggactataaa gatcccaggc gtttccccct ggtagctccc tcatgcgctc
     2461 tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc ggtttctcat
     2521 tccacgcctg acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga
     2581 accccccgtt cagtccgacc gctgcgcctt atccggtaac tatcatcttg agtccaaccc
     2641 ggaaagacac gacttatcgc cactggcagc agccattggt aagaggatgt acaagagatt
     2701 actaacgcag agttcttgaa gtatcagccc aactacggct aaactggaag gacgaatttg
     2761 gtggcagcgg tcttgtacac cctgttacca cggttcagaa gttccccaac ttactgaacc
     2821 atcgaaaaac cacctcccca ggtggttttt tcgtttctgg gtcaagagat tacgactccc
     2881 acccgagaat ctcaagaaga tccttcaact ctgtgttcaa aacactgttt aaaacagcta
     2941 taagccttca agatagtttc agaaatacaa tgctatttca ctctctggaa aacaaaccaa
     3001 aaaggtcaaa aaaatgataa gaaagatttt ttttgcttct gcaatcgtaa tagccatctc
     3061 tggctgtaca gcaatggata aattggcagg aatgggtgtt gtttctcagc aaacatcaac
     3121 ctttgataac tcgaccgtta tagaggtatc tccaaattcg ctatacgatc ctaacagcac
     3181 ttggggaaca caacttcagt tgggcgcgat atggtctagt gcctatccag aagaggttgg
     3241 gctaattctt tcctacaact cgaatgtatc tagcggaaat gccgcatact taggtttgac
     3301 ggggattgat ataaatattg atggcaaaat atccagctat aaagcacagc agcaaactaa
     3361 tctaagcagt agcgcatata actccgtatc taaaacgatc tatacctcta gcaagaacac
     3421 tgttgttatc ccctataaat tgctggagag catggtatca gctaaaaact gccgcattcg
     3481 catacacaca agccaaggaa atcaagacat cgacttctcg gcgcaaagca tccctggagg
     3541 taaagcgaca gcgatcgttt ccattaaaga gttcatggtc aaagtcgaaa gttttaaata
     3601 aggacacgta agcccaccta tatctactaa cttagtgtta ataggcatag gtggaaattt
     3661 ttgtctgcac gaaaaaaccc gacgatgccg ggtgtttagt gttaattcag caaattatag
     3721 cgatacagct gcttttcaaa atcctgcttc atgctcacaa acaacagtat ttcgatgttc
     3781 gttccgtcaa aatcgtaaag caccctgtat tcactctcaa catcgagccg ctcacgtaaa
     3841 agcatacctc gatcctgtaa gtggaaattg tagtgataac gttcagggtc ttggataatg
     3901 caggcaactg attcctgaag taagttatca accagatcac cggccttgag tgacccaatg
     3961 tatccactct tgtaagactc gatatcagct aaacattgat atgccatcgg cgcgattgaa
     4021 accgtgtatt gctgggacac taaacacctc tctgttattt tctagcggca cgcaacctcc
     4081 ctaagacctc ttctggggtc atgcctttgc cttctgtgat ttccttttta gccaacgttg
     4141 ccagcttaaa aagggcgttg atattgcgtt cttctctcat ctcacgaact tcagcatcac
     4201 gttctgctgc ggtttggatg aataactcag ctactccgtt tttagtgacg taaacacctc
     4261 cttcaaaggt ttgtgcattt ccgagactgt ctcttgcgag tttctgggac atggtctggt
     4321 tcataggcat ttttttctca tcatataggg gcgcttccgg cgagaacggc gctgcacgat
     4381 tcaagggtca tagtttccgg tttgtggttt caggtttcag gtttcaggtt tcagtgttga
     4441 tttattaggc cagtacaaat tctcgctatg gcacatggtg gccagtgtcc gtgctttgaa
     4501 tagagtttat cagttggtgt ataaattgag tacatatttt tacacagaaa ggtgaaagaa
     4561 gggaaaatta gtttaattca gaatcattta ccataacatc tcttaccggc accgctccgg
     4621 acgggttcag cgcgaatgcg ccgtcagccc ggaaaaaaat acagttaact cccc
//
