LOCUS       CP082517                4673 bp    DNA     circular BCT 12-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            FSIS1606077 plasmid pF18S004-2, complete sequence.
ACCESSION   CP082517
VERSION     CP082517.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN04605174
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 4673)
  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 4673)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4673)
  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                     :: F18S004
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 585x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 14:01:41
            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)                     :: 4,837
            CDSs (total)                      :: 4,715
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            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)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 41 of 110
            Pseudo Genes (incomplete)         :: 69 of 110
            Pseudo Genes (internal stop)      :: 20 of 110
            Pseudo Genes (multiple problems)  :: 17 of 110
            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..4673
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="FSIS1606077"
                     /serovar="Typhimurium"
                     /isolation_source="animal-chicken-young chicken"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pF18S004-2"
                     /geo_loc_name="USA:WV"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            join(4447..4673,1..42)
                     /locus_tag="A4R48_024150"
                     /pseudo=""
     CDS             join(4447..4673,1..42)
                     /locus_tag="A4R48_024150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019080654.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            57..395
                     /locus_tag="A4R48_024155"
     CDS             57..395
                     /locus_tag="A4R48_024155"
                     /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="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="UAE08030.1"
                     /translation="MSQQYTVSIAPMAYQCLADIESYKSGYIGSLKAGDLVDNLLQESV
                     ACIIQDPERYHYNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQ
                     LYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(496..1083)
                     /locus_tag="A4R48_024160"
     CDS             complement(496..1083)
                     /locus_tag="A4R48_024160"
                     /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="UAE08031.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            2166..2489
                     /locus_tag="A4R48_024165"
     CDS             2166..2489
                     /locus_tag="A4R48_024165"
                     /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="UAE08032.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2479..3192
                     /locus_tag="A4R48_024170"
                     /pseudo=""
     CDS             2479..3192
                     /locus_tag="A4R48_024170"
                     /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            3167..3652
                     /locus_tag="A4R48_024175"
     CDS             3167..3652
                     /locus_tag="A4R48_024175"
                     /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="UAE08027.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3656..3865
                     /locus_tag="A4R48_024180"
     CDS             3656..3865
                     /locus_tag="A4R48_024180"
                     /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="UAE08028.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3962..4144
                     /locus_tag="A4R48_024185"
     CDS             3962..4144
                     /locus_tag="A4R48_024185"
                     /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="UAE08029.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     Typing          1878..2057
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          complement(1416..1895)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.309"
                     /coverage="92.0"
                     /evalue="2.1e-176"
     Typing          2480..3975
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccagaagagg tcttagggag gttgcgtgcc gctagaaaat aacagagagg tgtttagtgt
       61 cccagcaata cacggtttca atcgcgccga tggcatatca atgtttagct gatatcgagt
      121 cttacaagag tggatacatt gggtcactca aggccggtga tctggttgat aacttacttc
      181 aggaatcagt tgcctgcatt atccaagacc ctgaacgtta tcactacaat ttccacttac
      241 aggatcgagg tatgctttta cgtgagcggc tcgatgttga gagtgaatac agggtgcttt
      301 acgattttga cggaacgaac atcgaaatac tgttgtttgt gagcatgaag caggattttg
      361 aaaagcagct gtatcgctat aatttgctga attaacacta aacacccggc atcgtcgggt
      421 tttttcgtgc agacaaaaat ttccacctat gcctattaac actaagttag tagatatagg
      481 tgggcttacg tgtccttatt taaaactttc gactttgacc atgaactctt taatggaaac
      541 gatcgctgtc gctttacctc cagggatgct ttgcgccgag aagtcgatgt cttgatttcc
      601 ttggcttgtg tgtatgcgaa tgcggcagtt tttagctgat accatgctct ccagcaattt
      661 ataggggata acaacagtgt tcttgctaga ggtatagatc gttttagata cggagttata
      721 tgcgctactg cttagattag tttgctgctg tgctttatag ctggatattt tgccatcaat
      781 atttatatca atccccgtca aacctaagta tgcggcattt ccgctagata cattcgagtt
      841 gtaggaaaga attagcccaa cctcttctgg ataggcacta gaccatatcg cgcccaactg
      901 aagttgtgtt ccccaagtgc tgttaggatc gtatagcgaa tttggagata cctctataac
      961 ggtcgagtta tcaaaggttg atgtttgctg agaaacaaca cccattcctg ccaatttatc
     1021 cattgctgta cagccagaga tggctattac gattgcagaa gcaaaaaaaa tctttcttat
     1081 catttttttg acctttttgg tttgttttcc agagagtgaa atagcattgt atttctgaaa
     1141 ctatcttgaa ggcttatagc tgttttaaac agtgttttga acacagagtt gaaggatctt
     1201 cttgagattc tcgggtggga gtcgtaatct cttgacccag aaacgaaaaa accacctggg
     1261 gaggtggttt ttcgatggtt cagtaagttg gggaacttct gaaccgtggt aacagggtgt
     1321 acaagaccgc tgccaccaaa ttcgtccttc cagtttagcc gtagttgggc tgatacttca
     1381 agaactctgc gttagtaatc tcttgtacat cctcttacca atggctgctg ccagtggcga
     1441 taagtcgtgt ctttccgggt tggactcaag atgatagtta ccggataagg cgcagcggtc
     1501 ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct acccggaact
     1561 gagtgtcagg cgtggaatga gaaaccgcgg ccataacagc ggaatgacac cggtaaaccg
     1621 aaaggcagga acaggagagc gcatgaggga gctaccaggg ggaaacgcct gggatcttta
     1681 tagtcctgtc gggtttcgcc gccactgatt tgagcgtcag atttcgtgat gctcgtcagg
     1741 ggggcggagc ctatggaaaa acggcaacgc cgcatccttt ttctgttcct ttctgatgtg
     1801 tcgccttccg ctttatctcg ttatccgtga gcctgtaacg cccgccgcag tctcacggca
     1861 ggagcgcagc gaccgagtga gcgaggaggc gtcatttcac ttttacctac attctgcact
     1921 tacgccccac agccgcattt ttcctctgtc acatgaagca cttccctgaa ttcccacttc
     1981 gatttactat attaagccag tatacactcc gctagcgcta cgtgactggt tcagggctgc
     2041 gccccgaaac ccgctaaaag ccactgacgc gcctgcggct tgcccaacac cgcgccgccc
     2101 gggaaagaat ttcccgcccg tcccggcgtt atcaggaggc cggattggca gataaacgca
     2161 gcaaaatgct cacgatgtgg gtgacggaag atgagcacag gcgtctgctg gagcgctgcg
     2221 agggtaaaca gctcgcggcc tggatgcgcc agacgtgcct ggacgagaag cccgcccgcg
     2281 ccggcaaact tccctcgatc tcgccggcgc tgcttcgtca gcttgccggc atgggaaaca
     2341 acctcaacca gattgcccgg caggttaacg ccggtggcgg cagcgggcac gaccgcgtgc
     2401 aggttgtcgc tgcgctgatg gccatcgacg caggactcga gcggctgcgg cacgccgtac
     2461 tggaaaaagg ggcagacgat gatcgttaag tttcacccga gagggcgcgg cggcggtgcc
     2521 ggtccggtgg attatctgct gggcaaagac cggcaccgcg acggcgccag cgttctgcag
     2581 gggaagccgg aggaagtccg ggagcttatc gatgcctcgc cttacgccaa aaagtacacc
     2641 tccggcgtcc tgtcatttgc cgaacaggac ttaccgcccg gacagcgtga aaagctgatg
     2701 gcgagcttcg agcgggttct gatgcccgga ctcgataaag atcagtacag cgtgctgtgg
     2761 gttgagcaca acgacaaagg gcggcttgag ctgaatttcc tgataccaaa cacggagctg
     2821 ctgaccggca ggcgtctcca gccgtattac gaccgcgccg accgtccgcg catcgatgcc
     2881 tggcagacca tcgtgaacgg tcggctgggg ctgcacgacc cgaacgcgcc ggagaaccgg
     2941 cgggcgctgg ccacgccgtc cgcgctgccg gaaacgaagc aggaagctgc ccagactatt
     3001 acgcggggtt tactggcctt agcctcgtcc ggggagctga aaacgcgaca ggacgtcact
     3061 gaggcgctgg aaaacgcagg ttttgaggtg gtgcgcacca caaaaagcag catcagcatt
     3121 gccgacccgg acggggggcg aaacatccga ctgaagggag ccatctatga acagtctttt
     3181 aacgctggcg aaggacttag agcagaaatc gaaagcgcag cagcagacta ccggcgagat
     3241 gctgaaagcc gcattcagcg agcacgagaa gtctgtcaga gcggaactga gcgaaagcga
     3301 gaagagaatc agcgccgcca tcctcgacca cgaccggaag ctgtcctcag ccatgagcca
     3361 gcgcacgaaa gggatgctgc gcatggtcag ccagacgtgg ctgaccatcg tgctggtctc
     3421 cgcgctgctg atcgcctcga gcgcgggcat tctgtggtgg caggggcagc agatactcga
     3481 gaactacacg accatccggg agcagaagaa cacgcaggcc atgctgtcag agaggaacag
     3541 cggtgtgcag ctcacgacct gcggagagca gagacgccgc tgcgtgaggg tgaacccgga
     3601 agcgggcggg ttcggagagg attcgagctg gatgatactg gcggggaaat agcacatgac
     3661 ggagctggaa aaacagctgc tgagcgcatt agagcagcta cagcaggact actcgaaaag
     3721 gctggacgag tgggagaacg ccttcgcgga atggcggacg atgtctggtc ttatgcaacg
     3781 ggagaacgcg gcgctgagcg agcgcgtcac gggcttgagc aggcaggtgc agagtttgag
     3841 cgagcagctt cgccggttgt cgtgagacta gacggcattg aagcacaccg ggagcatgag
     3901 cgggcggtgc agcaccagaa aacgctggag cttgaacgat cgcagcggca gcggacgtac
     3961 aatggaccgt cgctgtaaca aaccggataa aacggggctt tcggcgaata tctgcggcga
     4021 aagccggtgc cattcacctg tctgcatggc tatgcattcg ggtgaaattt atcaggcgca
     4081 ggcggcgcgt tttaccgggg agttaactgt atttttttcc gggctgacgg cgcattcgcg
     4141 ctgaacccgt ccggagcggt gccggtaaga gatgttatgg taaatgattc tgaattaaac
     4201 taattttccc ttctttcacc tttctgtgta aaaatatgta ctcaatttat acaccaactg
     4261 ataaactcta ttcaaagcac ggacactggc caccatgtgc catagcgaga atttgtactg
     4321 gcctaataaa tcaacactga aacctgaaac ctgaaacctg aaaccacaaa ccggaaacta
     4381 tgacccttga atcgtgcagc gccgttctcg ccggaagcgc ccctatatga tgagaaaaaa
     4441 atgcctatga accagaccat gtcccagaaa ctcgcaagag acagtctcgg aaatgcacaa
     4501 acctttgaag gaggtgttta cgtcactaaa aacggagtag ctgagttatt catccaaacc
     4561 gcagcagaac gtgatgctga agttcgtgag atgagagaag aacgcaatat caacgccctt
     4621 tttaagctgg caacgttggc taaaaaggaa atcacagaag gcaaaggcat gac
//
