LOCUS       CP082422                4074 bp    DNA     circular BCT 05-MAY-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            FSIS11704063 plasmid pF18S031-3, complete sequence.
ACCESSION   CP082422
VERSION     CP082422.2
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN07605937
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 4074)
  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 4074)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4074)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
REFERENCE   4  (bases 1 to 4074)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
  REMARK    Nucleotide sequence updated by submitter
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 260x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/28/2023 11:44:12
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,254
            CDSs (total)                      :: 5,133
            Genes (coding)                    :: 4,996
            CDSs (with protein)               :: 4,996
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 53 of 137
            Pseudo Genes (incomplete)         :: 90 of 137
            Pseudo Genes (internal stop)      :: 26 of 137
            Pseudo Genes (multiple problems)  :: 30 of 137
            Pseudo Genes (short protein)      :: 1 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            On May 5, 2023 this sequence version replaced CP082422.1.
            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..4074
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704063"
                     /serovar="Typhimurium"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pF18S031-3"
                     /geo_loc_name="USA:MN"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            complement(238..492)
                     /gene="mobC"
                     /locus_tag="CLJ14_023820"
     CDS             complement(238..492)
                     /gene="mobC"
                     /locus_tag="CLJ14_023820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="UAF10653.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            671..2836
                     /gene="mobQ"
                     /locus_tag="CLJ14_023815"
     CDS             671..2836
                     /gene="mobQ"
                     /locus_tag="CLJ14_023815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="UAF10652.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQKEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRAQL
                     LKREDELRRKELEDTERSRAERRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFESVDLIRDRSGYICDRSEIGQHPPLQRIYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            complement(3078..3779)
                     /locus_tag="CLJ14_023825"
     CDS             complement(3078..3779)
                     /locus_tag="CLJ14_023825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003887 - DNA-directed DNA polymerase activity [Evidence
                     IEA]; GO_process: GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAF10654.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(494..670)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          671..1029
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          complement(3080..3779)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.287"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          585..2827
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.46"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggggtgctg aaaataaaaa tccaataaaa acaatgtgtt gcaaaaaacc aggattgaag
       61 attccgaata caccccctcc aaccctgtgg aaatccagta ttcatgcggg ttcagcgcat
      121 atcacctgtc gaaaaaccgt gcgtatgtgc tcaacatggc gactgattca cttccgcttc
      181 ctcgcccact cgctcgctaa cgctcggtcg ctgggctgcg gcgagcggac gatacaatca
      241 ctgctctggc agcgcctcca gctcgttaat cagcggcagt attcgcgtca catcagcctg
      301 ccgtgtcacc tctgccttca ggaactggag taaccaggct cgcaactgca cttcctccgg
      361 ctttctgacc tttgccagca atgctgcacc cacaatgacc ttctgcgctg tgtccaggct
      421 ccggctcttc gccttcaggc gctgtaatct cgcctcagca tcagcaatct tctgttcgag
      481 cgttctgctc atgatgtaac tccatgcgcg atgaaaaatc gcattttagc gcgtcactgg
      541 tagtttaaaa actgagctgg cataatgcac ggcaaatcac gaagtgcgca cttatacaat
      601 ctccactccg tttcgattgt gtgcgccctg cggggctgaa agaaaactgc aaaaaggcat
      661 tacggcagaa atggcgattt atcatctcag tatgaaaatc atctccagaa gcaacggcta
      721 cagcgccgtt gcttctgctg cctatcgttc tggttcacta atgcttgatg agcgtaccgg
      781 actgactcac gactacaccc gcaaaagcgg tgtggctgag gctgtgattc tgacccccgc
      841 gacagcccct gcctggtgta cgaaccgtgc cgaactctgg aatgccgttg agaaggccga
      901 acgccggaag aactcacaac ttgcgcggga aattgaactc gccatccccc acgaactgcc
      961 gcaggatgcc gcacgggaaa ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg
     1021 catgattgct gatgtggcgt tccatcacat ggataaaaca aatccccatg cgcacattat
     1081 gctgaccacg agggctgtcg gacctgcggg gttcggcgga aaggtcaggg actggaacga
     1141 ccggacacat gccgagacgt ggcgtgcatc atgggctgac catgcaaaca gggcactggc
     1201 gaacgccggt tatcagaaag agatagacca tcgttcatac gagcgacagg ggcttgagaa
     1261 aacgccgggt attcacctcg gaaagtctgc ctgtgcgatg gaaacacgcg gtatcgaaac
     1321 agaacgcggc gaacagaatc gtctgattaa caggcttaac ctggaaatac agatttcccg
     1381 caccgaactc aggaacagcg ggctgacaga gcctgcccgc cgtgtggctg accttctgaa
     1441 tatcgggctt cctgacaacg caacttcgta cacactacgt gacatcatcg aagcgttgcc
     1501 gaaggacagt aacgcggcat ggaaactcac cagtaacgcc atgtcgatga tggcagatat
     1561 gcaggcgacg cgcagacgct gggaagagct gaacaccgaa cgaaaggaag cgatgagcca
     1621 tgctgccagc ctgaaaaaat catcgccgtt ttcgtccggt ttttcccgta ttcccctgat
     1681 gcaatgggct gcaccggaat accgtagtga gcagggaaaa atccagtctc tgagccagca
     1741 aatggaaaaa ttgcgacagc attaccggaa ggtggagaaa caggacattc ccgcgagtca
     1801 gacggcattt gaaaaacagt ggcagcagtg gggggaatcc ggccttgcag ctctcagagc
     1861 ccagttgctt aaacgtgaag atgaattacg ccggaaggag ctggaggata cagaacgtag
     1921 tcgcgcggag cgacgagcgg aacagctcag gaaaaatgac aatgccgtta tggattcagg
     1981 ggtgctgaga gcagtcgtta cggggtatgg cgaggctccc atgcctggta acggggaaat
     2041 gacttgttac cttctgcttc acaaccggaa cggagaatac acgctctggg ggaacgagct
     2101 ggagaaatac cgcaccagga tctttgagag tgttgattta atacgtgaca ggagtggtta
     2161 tatctgtgac cgaagcgaaa tcggtcaaca tccaccactg caacgtattt attcctctgc
     2221 gacctttgag caacttctga cgcaggtttg ccagacatgg ccgcaacata cccgcaatct
     2281 ccgccagccg aagacatggc cggagtcttt ctgtcttgga gaagaccgcc agccagccat
     2341 gccatcactg gcagcaagga aggtggattt tacgcaggga cgtctgccac cgacgctgat
     2401 gccggtcatg agttctgtcg accgggaaac ccgccagctt cagcttttgc tggtcatggg
     2461 cgtggatgac tctctgggcg gtgttgtccg gcttaatggt acgctgtatc ccgcgtttgc
     2521 cgttccctca gccgataaca gccagctggt tatcagtgca ctgaccgata aggggttacg
     2581 gtatgcaggg tatggtgttg ccgtaaatca tgatgcagac agccacatat cacctgcacc
     2641 ggaacttatg gagtttcatc tgaaaacccg tgaggcaccg ctttttgctg tcgtcaacac
     2701 accagaaaaa cagccggatc atctgttccg ctcgctgggt ttcaatcgta cctgggacga
     2761 atggcggcgc gaggaagatg cacgaacaca cgccaccgag aggagacctg atcgcggttg
     2821 gtcacaggga atgtgaacaa tattttgttt tgtttaacat cgtgttatgt tcgtcgatgt
     2881 tcatcgacag ggatgaatgc aagaagcaca ctcacatagc gcaaacatag ttttgttttt
     2941 ccgcccccaa aaattggggg ttcttttttt gctgcatcag agcgtttttg acgcaacttt
     3001 tcacttcaat agtaccttcg cattcctgac acaagaaaaa cgcgacagtg agcgttttag
     3061 gtgccttaaa atcgattcta gatcgtcatc ttgatctgtt tgtcttcctt gaagcgaaag
     3121 tgcagggcta caaccgtgcg cccctttttg atcgtctcaa ccgttacaac cagatcgctt
     3181 ttttcgttca gttcggcgat ggctggcttg attatcatct tattcaagtc tttgaattgt
     3241 tgatatttat cttcaacggc aagcatggtt cggaaatcat cgatagctat cgttctgtca
     3301 ccggtgctgc ggaactgctg gagcagctcg taaatgcgga tgctgtaggt gctggagagg
     3361 ctggagacgt tcttcacgac tacccgcgta aactgcccct tgagctgtgt cagatacggc
     3421 atgatggcat cggagaaggt gatctctact ttcgcctcac ctttgaaata ctgcgcccgg
     3481 tactgcaccc agcggaactc ttctcgtttt tcctcgttct tgatgattac tgacctgtcc
     3541 cagaggcgat ctatcgcttc cttgagccta gcttcagcgt gctgccgtcc catgtcagga
     3601 aaggcatcat gaaactctgc agccgtgatg gtcatggttt tttgttcatc cggcgaaggg
     3661 gaatcttctc cggatttcag gcggctgata cagaccagca ggaagcgctg ttcctgcaaa
     3721 gtgagcttgt agcttgcctc gataagggcg tttgatttgt aagctatcag atctgacatt
     3781 tcgcttgctc gttgctattg gtggcgtttt tttactgtac gccacctatc atattggtgg
     3841 aagttttttt tttgcaaccc cttttttctg tggattacac ccccaaaagc tccacttatc
     3901 acccccaaaa gctccaccta tcacccccaa aagctccacc tatcaccccc aaaagctcca
     3961 cctatctcgc cagaacacct ttaaaatcat gtggttacaa gacctaaaaa ggttttaaaa
     4021 aaaaagatct aaaaataaga tcttaaaaac ttaacggcga gcctgtggat aact
//
