LOCUS       CP123691                4703 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg strain
            FSIS11813680 plasmid pFSIS11813680-3, complete sequence.
ACCESSION   CP123691
VERSION     CP123691.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN09954714
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Senftenberg
  ORGANISM  Salmonella enterica subsp. enterica serovar Senftenberg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4703)
  AUTHORS   Ge,B., Mukherjee,S., Li,C., Harrison,L.B., Hsu,C.H., Tran,T.T.,
            Whichard,J.M., Dessai,U., Singh,R., Gilbert,J.M., Strain,E.A.,
            McDermott,P.F. and Zhao,S.
  TITLE     Genomic analysis of azithromycin-resistant Salmonella from food
            animals at slaughter and processing, and retail meats, 2011-2021,
            United States
  JOURNAL   Microbiol Spectr 12 (1), e0348523 (2024)
   PUBMED   37991374
REFERENCE   2  (bases 1 to 4703)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (05-SEP-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4703)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
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                   :: 257x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 10:46:17
            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)                     :: 4,755
            CDSs (total)                      :: 4,635
            Genes (coding)                    :: 4,519
            CDSs (with protein)               :: 4,519
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 44 of 116
            Pseudo Genes (incomplete)         :: 83 of 116
            Pseudo Genes (internal stop)      :: 18 of 116
            Pseudo Genes (multiple problems)  :: 25 of 116
            Pseudo Genes (short protein)      :: 1 of 116
            CRISPR Arrays                     :: 2
            ##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..4703
                     /organism="Salmonella enterica subsp. enterica serovar
                     Senftenberg"
                     /mol_type="genomic DNA"
                     /strain="FSIS11813680"
                     /serovar="Senftenberg"
                     /isolation_source="animal-cattle-steer"
                     /sub_species="enterica"
                     /db_xref="taxon:28150"
                     /plasmid="pFSIS11813680-3"
                     /geo_loc_name="USA:KS"
                     /collection_date="2018"
                     /collected_by="USDA-FSIS"
     gene            complement(36..359)
                     /locus_tag="D3F45_23745"
     CDS             complement(36..359)
                     /locus_tag="D3F45_23745"
                     /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="WGN65004.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRPLAAWMRQTCLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNTGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1006..1167
                     /locus_tag="D3F45_23750"
     CDS             1006..1167
                     /locus_tag="D3F45_23750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WGN65001.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNGFRGVSLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(1508..2002)
                     /locus_tag="D3F45_23755"
     CDS             complement(1508..2002)
                     /locus_tag="D3F45_23755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000929317.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN65002.1"
                     /translation="MAGTVWNDVNTGREVFSMTHLHPQLHKVEVSGVLVEIEISFGFHV
                     FTDQKQVGKVMSFRGETRHFCQERYEGSKTIVQRILSAIENGEYITAFISKGQGQRYYH
                     LNHHDDFILMEIRKPQGKDNCLRIHVVTAYTMDEWGVVNKGRNLKFRYVLEQRLQGKKI
                     V"
                     /name="hypothetical protein"
     gene            complement(2006..2524)
                     /locus_tag="D3F45_23760"
     CDS             complement(2006..2524)
                     /locus_tag="D3F45_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640499.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN65003.1"
                     /translation="MSVRAQRAGKRNQSERRIELINTLWEGEEIETWDRNDRPRNDGFI
                     TVPRYLPLLGVLMDELSKGSPLSSTYLALWFRGSDEGLIEIRDKTVLALESGFASARGV
                     TTWTGRMRKLKELGFISCREGSSGEFHNVLIVHPLVAVKKLLDEGKITKGKTYNTFAER
                     VIEVKSSWE"
                     /name="hypothetical protein"
     gene            complement(3348..3563)
                     /locus_tag="D3F45_23765"
     CDS             complement(3348..3563)
                     /locus_tag="D3F45_23765"
                     /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="WGN64999.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3570..4061)
                     /locus_tag="D3F45_23770"
     CDS             complement(3570..4061)
                     /locus_tag="D3F45_23770"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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="WGN65000.1"
                     /translation="MSNLLTLAKDLEQQSKAQQKSTGEMLKAAFCEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMKTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            complement(4099..4530)
                     /locus_tag="D3F45_23775"
                     /pseudo=""
     CDS             complement(4099..4530)
                     /locus_tag="D3F45_23775"
                     /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"
     Typing          complement(473..645)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="4.3800000000000006e-64"
     Typing          570..1120
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.514"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(43..359)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.509"
                     /coverage="99.0"
                     /evalue="7.35e-60"
     Typing          complement(3257..4701)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.628"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 gcccggcgcc accgccgcga ccgcgtggat gaaatttaac gatcatcgtc cgttcctttc
       61 tcaagaacgg cgtgccgcag ccgctcaagt ccggcatcga tggccatcag cgccgccaca
      121 atctgtaccc tgtcatggcc agtaccgccg ccggtgttaa cacggcgggc tatctggttc
      181 aggttattgc ccatgccggc aagctggcgc agcagcgccg gcgaaattga ggggagcttt
      241 ccggtgcgcg caggcttttc gtccaggcag gtctgccgca tccaggccgc cagcggcctg
      301 ccgtcacagc gctcaagcag ccgccggtgc tcgtcctccg tcacccacat ggtgagcatc
      361 ttgttccgtt tctctgacaa accggcctcc tgataacgcc gggacgggcg ggaaagcctt
      421 tcccggtcgg cgcggggttg gacaagccgc aggcgcgtca ggcttttggc gggtttcggg
      481 gcgcagccct gaaccagtca cgtagcgcta gcggagtgta tactggctta gtatgttacg
      541 acggggtgag ggttcaggaa agtgcttcat gtggcaggag aaaaatgcag cagcggagcg
      601 tcagcagaat atgtgataca ggatatattc cgcttcctcg ctcactgact cgctgcgctc
      661 ggtcgttcgg ctgcggcgag cggtaccaac ttacaggcgg ggcggaaatt tcctgggaga
      721 tgccaggaag aagcttaacg gagaagcgat aaggccacgg cgaagccgtt tttccatagg
      781 ctccgccccc ctgacaagca tcacgaaatc tgacgctcaa atcagtggtg gcgaaacccg
      841 acaggactta aagataccag gcgtttcccc ctggtggctc cctcgtgcgc tctcctgttc
      901 ctgcctttcg gtttaccggt gtcattccgc tgttatggcc gcgtttatct cattccacgc
      961 ctgacactca gttccgggta ggcagttcgc tccaagctgg actgtatgca cgaacccccc
     1021 gttcagtccg actaccacgc ccgttccggt aactatcaac ttgagtccaa cccggaaaga
     1081 cacgacaaat cgccagtggc ggtagccatt ggtaacggat ttagaggagt tagtcttgaa
     1141 gttatgcgcc tgttaaggct aaactgaaag gacagatttg gttactgcgc tcctccaagc
     1201 cagttaccgc ggttcaaaga gttggtagct ctgagaacct tcgaaaaacc gccttgcagg
     1261 gcggtttttt cgtttacagg acaagagact acgacgatag acaaaggatc tcaagaagat
     1321 catgataaac ccgtgaagtt gacaagaggc atgggtaagt agacaatata cctgttagca
     1381 caaaccggaa ccttgaaaga ggggtgctga tgccggggga aaaccctcct agccagtgag
     1441 caggataact aaaggccaga ccgaaatttt tgcagtaaaa caaaggcgcc tagggcgctt
     1501 tttgttttta tacgattttc ttcccctgca acctctgctc cagaacatac ctgaacttca
     1561 aattgcgtcc tttgttaacc accccccatt catccatcgt atacgctgta acaacgtgta
     1621 ttcgaagaca attatcttta ccttgaggct ttcttatctc cattagaatg aagtcatcat
     1681 gatggttaag gtggtaatat cgctgccctt gtcccttgga aataaaggcc gttatgtact
     1741 ctccattttc tatcgctgac agtatcctct gcacgatagt cttacttcct tcgtatcttt
     1801 cttggcagaa atgtctagtt tcccctctga aactcattac ctttccgacc tgtttttggt
     1861 cagtaaatac atgaaacccg aagctaatct caatctcaac cagtacccca gaaacctcaa
     1921 ccttatgcag ctgagggtgc aggtgtgtca tcgagaaaac ttcacgccct gtattaacat
     1981 cattccatac cgtacctgcc atttcttact cccatgagga cttcacctcg attacccgtt
     2041 cagcaaaagt gttataggtt ttccctttcg ttattttccc ttcatccagt agtttcttta
     2101 ccgcaaccag cggatgaaca atcaacacgt tgtggaactc accggagcta ccttcccggc
     2161 atgatataaa tcccagctct tttaatttcc gcattctccc cgtccatgtt gttacccccc
     2221 ttgcactggc aaagcctgat tctaaagcca gcacagtctt atcccttatc tctatcaggc
     2281 cttcgtctga acccctgaac cacagcgcta ggtaggtact tgaaagtggg cttccctttg
     2341 ataactcatc cataagaaca cctagtaatg gaagataacg aggtactgtt atgaagccat
     2401 cgtttcgagg tcggtcatta cgatcccatg tttcaatttc ctccccttcc cataatgtat
     2461 ttatcagttc gattcttctt tcagactggt tacgtttccc tgctctttgt gccctgactg
     2521 acatactcgc ctcctgttaa tgcgtgagag aaatttacca aaaaaccctt ataaatcaat
     2581 aacttttata aattcccttg aacaattact tccggttttt atttttttta atcataaaaa
     2641 atgcaatatt cattacacaa aaggcggtta caagtaataa atattacaaa cacaaaatgc
     2701 atttatatga tttaaaaaga gtttttattt aattgcggtg ctccatgtgc tcatcgtgct
     2761 ccatgtgctt ctggtgctcc cttgtgctcc atggggttgt agggggcaag gaggggggga
     2821 gaaatcgaaa aataaattaa gagtcaccat gctggttact cgcatttacc ataacatccg
     2881 ttgcccgcac cgctccggac gggttcgcca caaacggggc ggcagtcagg taaaaccggc
     2941 aacaaaccac ccgatacacc gccccgttcg tgacagataa attttacccg actgcatagc
     3001 catgcaacca gatgcatggc gtgtaaagtc acactaaaat cagcgcgaac gccttaaaaa
     3061 caggtaaatg cttctccagc cagtcccaca gcccggccgc cagatacagg cagttaagta
     3121 cagcttcaat gacgttaagc aatttcataa ttcccccccc caggtatagg ccgtgatctt
     3181 tttgatcacg aacctattta gcgggagaag taagagcccc tcttcgtgcg ggttgtcagc
     3241 tgcctggatg gtttaaagtg tcggcccgcg gtaggttttc tgcggctggc gctccagctc
     3301 cagtgttttc tgatactcat tctccctctg ccggagctcg atggcattca gttcccggac
     3361 aagcggcgca gctgctcgct taaactcagc acctgcgtgc tcaagtccga cacgcgctcg
     3421 ttcagcaccg cgttctcccg ttgcataagc ccacacatgc tccgccattc cgcgaaggcg
     3481 ctctcccatt cgtccagcct ttgcgagtag tcctgctgta gctgctctaa tgcgctcagc
     3541 aactgctttt ccagctctgt catcttccgc tactcctgtt tcaggcggat ccatgtcgtc
     3601 ccgtcgtaag ggatggcttc ggttttcatc cccggcggca ggataagaaa cctccggccg
     3661 tcgctgctct cctgatagcg cactccccac gtccgggcgg tcattttcgc cagggtatct
     3721 tcctgctgac gaagatgcgt gtaattgtcg gttatctgct gcccctgcca ccacagtatg
     3781 ctcccgctcg tgccgatcag cagcgctgac accatcagga tggtgagcca tgtccgcccg
     3841 gcagtccgca gtacgctccg ccggtttttc tccatcgcct cgctcatact ctgctcgtgg
     3901 gcgaggatgg cgtcgctgat tctcctcgcg cttgcgctca gttccgctct gacagactgc
     3961 tcgtgctcgc agaatgcggc tttcagcatc tcgccggtac tcttctgctg cgctttcgat
     4021 tgctgctcta agtccttcgc tagcgttaaa agattgctca tagatagctc ccttcagtcg
     4081 gatgtttcgc cccccgtccg ggtcggcaat gctgatactg cttttcgtgg tgcgcaccac
     4141 ctcaaaacct gcaccttcaa gagtgtcagt gacatcctga cggcttttca gctccccgga
     4201 cgaggctaag ctcagtagtc cccgggtaat ggcttcggcg gcctcctgcg tcgttttcgg
     4261 cagcccggac ggcgtgacca gcgcccggcg gttttccggc gcgttcgggt cgtgcagccc
     4321 cagtctgccg ttcacgatag tctgccaggc atcgatgcgc ggccggtcgg cgcggtcgta
     4381 gtaaggctgg agccgcctgc cggtcagcag ctcggtattg gggatcagaa agttcagctc
     4441 cagacgcccc ttgtccgcgt gctccaccca cagaatgctg tactgatctt tatcgagtcc
     4501 gggcatcaga acccgctcga agctggccat cagtttttcc cgctggccgg gagggagatc
     4561 ggcctccgca aacgacagga cgccggaggt gtatttctta acgtaaggcg acgcgtcaat
     4621 cagctcccgg acttcttccg gcttcccctg taggacggtg gcgccttcac gctgccggtc
     4681 tttacccagc agatagtcca ccg
//
