LOCUS       CP082743                4674 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            strain CVM N16S070 plasmid pN16S070-3, complete sequence.
ACCESSION   CP082743
VERSION     CP082743.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN08113949
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4674)
  AUTHORS   Li,C., Tyson,G., Hsu,C.-H., Harrison,L., Strain,E., Tran,T.-T.,
            Tillman,G., Dessai,U., McDermott,P. and Zhao,S.
  TITLE     Long-read sequencing reveals evolution and acquisition of
            antimicrobial resistance and virulence genes in Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4674)
  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 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                   :: 671x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/31/2021 18:30:13
            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)                     :: 4,994
            CDSs (total)                      :: 4,872
            Genes (coding)                    :: 4,744
            CDSs (with protein)               :: 4,744
            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)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 42 of 128
            Pseudo Genes (incomplete)         :: 85 of 128
            Pseudo Genes (internal stop)      :: 24 of 128
            Pseudo Genes (multiple problems)  :: 20 of 128
            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 var. 5-"
                     /mol_type="genomic DNA"
                     /strain="CVM N16S070"
                     /serovar="Typhimurium var. 5-"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:1620419"
                     /plasmid="pN16S070-3"
                     /geo_loc_name="USA:NM"
                     /collection_date="2016"
                     /collected_by="FDA"
     gene            join(4560..4674,1..209)
                     /locus_tag="CWX32_024870"
     CDS             join(4560..4674,1..209)
                     /locus_tag="CWX32_024870"
                     /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="UAG07346.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            199..912
                     /locus_tag="CWX32_024875"
                     /pseudo=""
     CDS             199..912
                     /locus_tag="CWX32_024875"
                     /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            887..1372
                     /locus_tag="CWX32_024880"
     CDS             887..1372
                     /locus_tag="CWX32_024880"
                     /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="UAG07347.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1376..1585
                     /locus_tag="CWX32_024885"
     CDS             1376..1585
                     /locus_tag="CWX32_024885"
                     /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="UAG07348.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1682..1864
                     /locus_tag="CWX32_024890"
     CDS             1682..1864
                     /locus_tag="CWX32_024890"
                     /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="UAG07349.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            2167..2436
                     /locus_tag="CWX32_024895"
     CDS             2167..2436
                     /locus_tag="CWX32_024895"
                     /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="UAG07350.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            2484..2789
                     /locus_tag="CWX32_024900"
     CDS             2484..2789
                     /locus_tag="CWX32_024900"
                     /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="UAG07351.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(2890..3477)
                     /locus_tag="CWX32_024905"
     CDS             complement(2890..3477)
                     /locus_tag="CWX32_024905"
                     /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="UAG07345.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     Typing          4272..4451
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          complement(3810..4289)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.309"
                     /coverage="92.0"
                     /evalue="2.1e-176"
     Typing          200..1695
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccggcaaact tccctcgatc tcgccggcgc tgcttcgtca gcttgccggc atgggaaaca
       61 acctcaacca gattgcccgg caggttaacg ccggtggcgg cagcgggcac gaccgcgtgc
      121 aggttgtcgc tgcgctgatg gccatcgacg caggactcga gcggctgcgg cacgccgtac
      181 tggaaaaagg ggcagacgat gatcgttaag tttcacccga gagggcgcgg cggcggtgcc
      241 ggtccggtgg attatctgct gggcaaagac cggcaccgcg acggcgccag cgttctgcag
      301 gggaagccgg aggaagtccg ggagcttatc gatgcctcgc cttacgccaa aaagtacacc
      361 tccggcgtcc tgtcatttgc cgaacaggac ttaccgcccg gacagcgtga aaagctgatg
      421 gcgagcttcg agcgggttct gatgcccgga ctcgataaag atcagtacag cgtgctgtgg
      481 gttgagcaca acgacaaagg gcggcttgag ctgaatttcc tgataccaaa cacggagctg
      541 ctgaccggca ggcgtctcca gccgtattac gaccgcgccg accgtccgcg catcgatgcc
      601 tggcagacca tcgtgaacgg tcggctgggg ctgcacgacc cgaacgcgcc ggagaaccgg
      661 cgggcgctgg ccacgccgtc cgcgctgccg gaaacgaagc aggaagctgc ccagactatt
      721 acgcggggtt tactggcctt agcctcgtcc ggggagctga aaacgcgaca ggacgtcact
      781 gaggcgctgg aaaacgcagg ttttgaggtg gtgcgcacca caaaaagcag catcagcatt
      841 gccgacccgg acggggggcg aaacatccga ctgaagggag ccatctatga acagtctttt
      901 aacgctggcg aaggacttag agcagaaatc gaaagcgcag cagcagacta ccggcgagat
      961 gctgaaagcc gcattcagcg agcacgagaa gtctgtcaga gcggaactga gcgaaagcga
     1021 gaagagaatc agcgccgcca tcctcgacca cgaccggaag ctgtcctcag ccatgagcca
     1081 gcgcacgaaa gggatgctgc gcatggtcag ccagacgtgg ctgaccatcg tgctggtctc
     1141 cgcgctgctg atcgcctcga gcgcgggcat tctgtggtgg caggggcagc agatactcga
     1201 gaactacacg accatccggg agcagaagaa cacgcaggcc atgctgtcag agaggaacag
     1261 cggtgtgcag ctcacgacct gcggagagca gagacgccgc tgcgtgaggg tgaacccgga
     1321 agcgggcggg ttcggagagg attcgagctg gatgatactg gcggggaaat agcacatgac
     1381 ggagctggaa aaacagctgc tgagcgcatt agagcagcta cagcaggact actcgaaaag
     1441 gctggacgag tgggagaacg ccttcgcgga atggcggacg atgtctggtc ttatgcaacg
     1501 ggagaacgcg gcgctgagcg agcgcgtcac gggcttgagc aggcaggtgc agagtttgag
     1561 cgagcagctt cgccggttgt cgtgagacta gacggcattg aagcacaccg ggagcatgag
     1621 cgggcggtgc agcaccagaa aacgctggag cttgaacgat cgcagcggca gcggacgtac
     1681 aatggaccgt cgctgtaaca aaccggataa aacggggctt tcggcgaata tctgcggcga
     1741 aagccggtgc cattcacctg tctgcatggc tatgcattcg ggtgaaattt atcaggcgca
     1801 ggcggcgcgt tttaccgggg agttaactgt atttttttcc gggctgacgg cgcattcgcg
     1861 ctgaacccgt ccggagcggt gccggtaaga gatgttatgg taaatgattc tgaattaaac
     1921 taattttccc ttctttcacc tttctgtgta aaaatatgta ctcaatttat acaccaactg
     1981 ataaactcta ttcaaagcac ggacactggc caccatgtgc catagcgaga atttgtactg
     2041 gcctaataaa tcaacactga aacctgaaac ctgaaacctg aaaccacaaa ccggaaacta
     2101 tgacccttga atcgtgcagc gccgttctcg ccggaagcgc ccctatatga tgagaaaaaa
     2161 atgcctatga accagaccat gtcccagaaa ctcgcaagag acagtctcgg aaatgcacaa
     2221 acctttgaag gaggtgttta cgtcactaaa aacggagtag ctgagttatt catccaaacc
     2281 gcagcagaac gtgatgctga agttcgtgag atgagagaag aacgcaatat caacgccctt
     2341 tttaagctgg caacgttggc taaaaaggaa atcacagaag gcaaaggcat gaccccagaa
     2401 gaggtcttag ggaggttgcg tgccgctaga aaataacaga gaggtgttta gtgtcccagc
     2461 aatacacggt ttcaatcgcg ccgatggcat atcaatgttt agctgatatc gagtcttaca
     2521 agagtggata cattgggtca ctcaaggccg gtgatctggt tgataactta cttcaggaat
     2581 cagttgcctg cattatccaa gaccctgaac gttatcacta caatttccac ttacaggatc
     2641 gaggtatgct tttacgtgag cggctcgatg ttgagagtga atacagggtg ctttacgatt
     2701 ttgacggaac gaacatcgaa atactgttgt ttgtgagcat gaagcaggat tttgaaaagc
     2761 agctgtatcg ctataatttg ctgaattaac actaaacacc cggcatcgtc gggttttttc
     2821 gtgcagacaa aaatttccac ctatgcctat taacactaag ttagtagata taggtgggct
     2881 tacgtgtcct tatttaaaac tttcgacttt gaccatgaac tctttaatgg aaacgatcgc
     2941 tgtcgcttta cctccaggga tgctttgcgc cgagaagtcg atgtcttgat ttccttggct
     3001 tgtgtgtatg cgaatgcggc agtttttagc tgataccatg ctctccagca atttataggg
     3061 gataacaaca gtgttcttgc tagaggtata gatcgtttta gatacggagt tatatgcgct
     3121 actgcttaga ttagtttgct gctgtgcttt atagctggat attttgccat caatatttat
     3181 atcaatcccc gtcaaaccta agtatgcggc atttccgcta gatacattcg agttgtagga
     3241 aagaattagc ccaacctctt ctggataggc actagaccat atcgcgccca actgaagttg
     3301 tgttccccaa gtgctgttag gatcgtatag cgaatttgga gatacctcta taacggtcga
     3361 gttatcaaag gttgatgttt gctgagaaac aacacccatt cctgccaatt tatccattgc
     3421 tgtacagcca gagatggcta ttacgattgc agaagcaaaa aaaatctttc ttatcatttt
     3481 tttgaccttt ttggtttgtt ttccagagag tgaaatagca ttgtatttct gaaactatct
     3541 tgaaggctta tagctgtttt aaacagtgtt ttgaacacag agttgaagga tcttcttgag
     3601 attctcgggt gggagtcgta atctcttgac ccagaaacga aaaaaccacc tggggaggtg
     3661 gtttttcgat ggttcagtaa gttggggaac ttctgaaccg tggtaacagg gtgtacaaga
     3721 ccgctgccac caaattcgtc cttccagttt agccgtagtt gggctgatac ttcaagaact
     3781 ctgcgttagt aatctcttgt acatcctctt accaatggct gctgccagtg gcgataagtc
     3841 gtgtctttcc gggttggact caagatgata gttaccggat aaggcgcagc ggtcggactg
     3901 aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg aactgagtgt
     3961 caggcgtgga atgagaaacc gcggccataa cagcggaatg acaccggtaa accgaaaggc
     4021 aggaacagga gagcgcatga gggagctacc agggggaaac gcctgggatc tttatagtcc
     4081 tgtcgggttt cgccgccact gatttgagcg tcagatttcg tgatgctcgt caggggggcg
     4141 gagcctatgg aaaaacggca acgccgcatc ctttttctgt tcctttctga tgtgtcgcct
     4201 tccgctttat ctcgttatcc gtgagcctgt aacgcccgcc gcagtctcac ggcaggagcg
     4261 cagcgaccga gtgagcgagg aggcgtcatt tcacttttac ctacattctg cacttacgcc
     4321 ccacagccgc atttttcctc tgtcacatga agcacttccc tgaattccca cttcgattta
     4381 ctatattaag ccagtataca ctccgctagc gctacgtgac tggttcaggg ctgcgccccg
     4441 aaacccgcta aaagccactg acgcgcctgc ggcttgccca acaccgcgcc gcccgggaaa
     4501 gaatttcccg cccgtcccgg cgttatcagg aggccggatt ggcagataaa cgcagcaaaa
     4561 tgctcacgat gtgggtgacg gaagatgagc acaggcgtct gctggagcgc tgcgagggta
     4621 aacagctcgc ggcctggatg cgccagacgt gcctggacga gaagcccgcc cgcg
//
