LOCUS       CP082412                5686 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain
            FSIS11704880 plasmid pF18S034-1, complete sequence.
ACCESSION   CP082412
VERSION     CP082412.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN08025063
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Derby
  ORGANISM  Salmonella enterica subsp. enterica serovar Derby
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5686)
  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 5686)
  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 5686)
  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                     :: F18S034
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 601x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 11:00:03
            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)                     :: 4,746
            CDSs (total)                      :: 4,628
            Genes (coding)                    :: 4,534
            CDSs (with protein)               :: 4,534
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 41 of 94
            Pseudo Genes (incomplete)         :: 53 of 94
            Pseudo Genes (internal stop)      :: 21 of 94
            Pseudo Genes (multiple problems)  :: 18 of 94
            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..5686
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704880"
                     /serovar="Derby"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pF18S034-1"
                     /geo_loc_name="USA:IA"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            complement(join(4774..5686,1..218))
                     /locus_tag="CVB56_023660"
     CDS             complement(join(4774..5686,1..218))
                     /locus_tag="CVB56_023660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="UAF25082.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            295..1362
                     /locus_tag="CVB56_023665"
     CDS             295..1362
                     /locus_tag="CVB56_023665"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="UAF25083.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPILE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKDIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            2005..2223
                     /locus_tag="CVB56_023670"
     CDS             2005..2223
                     /locus_tag="CVB56_023670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001488611.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAF25086.1"
                     /translation="MFFPALSPDSVDNRIAVFEQADSARRSRTTERSESVSEEAEKRRD
                     VHFLLTHLCGISHPAWCTFHTMRPDAE"
                     /name="hypothetical protein"
     gene            complement(2375..2566)
                     /locus_tag="CVB56_023675"
     CDS             complement(2375..2566)
                     /locus_tag="CVB56_023675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="UAF25084.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2631..2954
                     /locus_tag="CVB56_023680"
     CDS             2631..2954
                     /locus_tag="CVB56_023680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="UAF25085.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2896..3654
                     /locus_tag="CVB56_023685"
                     /pseudo=""
     CDS             2896..3654
                     /locus_tag="CVB56_023685"
                     /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            3632..4150
                     /locus_tag="CVB56_023690"
     CDS             3632..4150
                     /locus_tag="CVB56_023690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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="UAF25080.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLTGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            4157..4390
                     /locus_tag="CVB56_023695"
     CDS             4157..4390
                     /locus_tag="CVB56_023695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="UAF25081.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2211..2290
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.67e-34"
     Typing          complement(1634..2179)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.364"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2945..4494
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.183"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttgacgttt ttgaatttat aactatttca ccaatcctgt ggcctgtcgc tactaatggt
       61 acacgccata catggtaccg atcatcgact tcaggtaacc caaaggaaaa tttatcagct
      121 aagtctaatt tctctaggtg caactttgct atttttttcg cctgagtcgt agaggttacc
      181 aaataacctc tgtttaagta attgttttta actgtcattt ttcctaacta tcgatctgtt
      241 accatacaac ctgctatctt agcatctcat ttttactatg tccatggtga ggatatgaat
      301 ttcaaggata aaaattgttt ccctaacgaa ctcatagcgt tggcgaaaat ttcaaaaaat
      361 gatgttttag ataagttcgg aacggatgtt tttaaaaagg ttgtttatga tgttttaaca
      421 ggtaaaaatg ttcgcgaatt cactgaaata ctaactcgta ctagattgtt agaaagcaat
      481 ctctcttttt ttgacttttt tgtggataaa atgaaagaag ggataacgcc aaagcagctt
      541 tatctctatg caaaaaatgc attatcgaac aagtcttatg ttaagtctaa tcaacctatt
      601 ctcgagtgga tggttatgat gacaaataaa cagacccaaa atgttttaag agatgagcat
      661 ggggatggtt ttgatagact tgctttaagg acgcaagaag aaatacttaa aataaaaaac
      721 gggtatgaag ataaaattgg agagatatct attggtgggc aaaaggtgtc tttagaagat
      781 ttttgctata ttattttatc tcttggttcg caaactttaa ctattagggg atctgagaaa
      841 tctcttcatg gtaaatattt tgaaaagcta atactcggtt ctttatttac aataatgggt
      901 tttgaatata aagaaaaaat tgaagaaggg ttaaatgcta aatgttttac tctttcaaca
      961 agagctgatg acagggagtc tgatgctact cttgttttta atgggaaggc gattagggtt
     1021 gacattggtt ttattggtag gggtaacaca gaaataagtt tggataaagt atctagattt
     1081 agacgaatgg atgatattgg cggagtgatg cataatataa gcacaatggt tattgttgac
     1141 gttattggtg atagaagtag aatagttaat atggctgaag agattgatgg taaagttgtt
     1201 gcgatgagtg acccgtattg ggttgcaaag gtctcttcct atattagttc gaaactgaat
     1261 gtagatgatc ttttagagga taaacctcaa cttaaagaca tacagtcttt tatatctgat
     1321 gcattagaga atgtagatct ggaaaaatac attaaattat aagagattgt aatccttgac
     1381 tgcgtgctta ttaaaagcat aatctctaca taaagaaaaa ccaccctggc aggtggtttt
     1441 tcaaaggtta gctaatcctg gcagattatc taaccaggta atctggctta agcagagcgc
     1501 agaccaccaa aacttgttct tctagtgtag ccagaatcag gctgatactt caagaactct
     1561 gttaccaact tataaatctc gctctgctaa cccggttacc aatggctgct gccagtggcg
     1621 tttttacgtg tctttccggg ttggactcaa gacgatagtt accggataag gcgcagcggt
     1681 cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgagc
     1741 cgagatacca acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg
     1801 agaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg
     1861 gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat
     1921 ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa acgccagcgg cgcggctttt
     1981 tttgcccttt gtctttttgc tcacatgttc tttccggcct tatcccctga ttctgtggat
     2041 aaccgtattg ccgtttttga gcaagcagac tccgctcgcc gcagtcgaac gaccgagcgc
     2101 agcgagtcag tgagcgagga agcggaaaag cgccgggacg tgcattttct ccttacgcat
     2161 ctgtgcggca tttcacaccc ggcatggtgc acttttcata caatgcgccc tgatgccgaa
     2221 taagtaagcc agtatacact ccgctatcgc tacgtgactg ggtcagggct gcgccccgac
     2281 acccgctaaa acccgctgac gcgtcctgac gggcttgtcg gctcccggca tccgctcaca
     2341 gacaagctgt gaccgtttcc gggagctgca tgtgtcagag gttttcaccg tcatccccga
     2401 aacgtgcgag gcagctgcgg taaagctcat cggcgtggtc gtgaagcgat tcacagatat
     2461 ctgcctgttc atctgcgtcc agttcgttaa gtttctccag cagcgttaat gtctggcctc
     2521 tgatgaaacg ggccatgtta agggcggttt tttcctgttt agtcactgat gcctccgtgt
     2581 aagggggatt tctgttcatg ggggtaatga taccgatgaa acgcgagagg atgctcacga
     2641 tacgggttac tgatgatgaa catgcccggt tactggaacg ctgtgagggt aaacaactgg
     2701 cggtatggat gcggcgggtc tgcctgggtg agccggttgc ccgttccggg aagctgccga
     2761 cactggcacc gccgttactg cgtcagctgg ccgccatcgg gaataacctg aatcagacag
     2821 cgaggaaggt gaacagcgga cagtggtctt ccggtgaccg ggttcaggta gtggccgcac
     2881 tgatggccat cggggatgag ctgcgccggc tgcgtctggc cgtcagggaa caggggacgc
     2941 gggatgatag ttaaatttca tgccagggga aaaggtggtg gcagtggtcc ggttgattac
     3001 ctgctgggaa gggagcgtaa ccgggaaggg gcaacggtgc ttcagggtaa tccggaagaa
     3061 gtccgggaac tcatcgatgc cacgccattt gcgaagaaat acacgtcagg tgttctgtcg
     3121 ttcgcggaga aggagctgcc gccgggagga cgtgaaaaag tgatggcgag ctttgagcgt
     3181 gtactgatgc ccggtctcga aaaaaatcag tacagcatcc tgtgggtgga gcaccaggac
     3241 aagggacggc ttgagctgaa ttttgtcatt ccgaacatgg agctacagag cggaaaacgc
     3301 ctccagccgt actacgaccg ggcagacagg ccgagaattg atgcctggca gacgctggtt
     3361 aatcaccatt acgggctgca tgaccccaac gccccggaga accgccggat actgactctc
     3421 cctgataacc tgccgaaaac gaaacaggcg cttgcagaga gcgtcacacg cgggatagac
     3481 gctctttatc atgtcgggga gataaaaggc cgtcaggatg tgattcaggc gctcacggag
     3541 gcagggattg aagtggtcag ggtgacgcga agcagtatca gcattgcaga cccgaacggc
     3601 gggaggaata tcaggctgaa aggagcattt tatgagcaat cttttacaga cgggcgcgga
     3661 gttcgagaaa aagctgaaag agagagccga atctacagag aaaatgctga acaacgagtt
     3721 caggaggctc ggcgagtctg tcagcgaggc tgtgacctca aacgagacga aaatcagaga
     3781 cgctatagcc ctgttcacag cctcgacaga gaaatcgctg gaaaaacacc gggaaggggt
     3841 gaaagaggcg atgatgcagc acaggaagga cgtgttaaag ctgacaggga atacgggcat
     3901 gatgttactg gggatagtct ttctcctgtt tacagcgagt ggcgggacgc tctggtatct
     3961 tggagggagg atacaggcga acctggaaga aatcaggaag caggaagaga cattgcagaa
     4021 actgaacgcg aagacatggg gcgtggagtt tgtgcaggac gggaacagga aattccttgt
     4081 ccttccgtac gggaaatcag cggaggtgat tccctttcag gggaaagagt gggtacatct
     4141 gaaggagtga cacagagtga cagagctgga aacacatttg ctgaacgcct tagagcagct
     4201 gcaacaggac tatatgcagc ggctgagcga atgggagagc gccttcgtgg aattgcagaa
     4261 gatgttttcg cttacgcaac gggacaacgc gatgctgaac gagcgggtca tgcagttgag
     4321 tcagcaggtg cagcacttga gcgagcagac agaacgcttg agccagttat acagcgagaa
     4381 ctggagataa gagaggaacg gctgatacag gagcgcgaac atgtgttatc cctggaacgg
     4441 gagcgtcagc cggaaataca ggaacgcacg ctggatggcc cttcgctggg atggtgaaac
     4501 catgaaaaat ggcaggttaa gtggattaag acaggctaat gtggtctgta ccatctggtt
     4561 gcataggtat tcatgcggtt aaaatttatc aggcgcgatt gcggcagttt ttcgggtggt
     4621 ttgttgccat ttttacctgt ctgctgctgt gatcgcgctg aacgcgtttt ggcggtgcgt
     4681 acaattaagg gattatggta aattcgacaa tgtggctgat gttgacgcgt aaataagccg
     4741 ccttaaggcg gcttttacca cagtaaagtt tgattaattt atgattttta aatcaccacc
     4801 tagcatggtt ccttctatga tcagatcaat atactgcttt gatatctcac acatcacaaa
     4861 tcttctgcct aaatcaattg ctgcttttgc tgttgttccc gatccagcaa aaggatctaa
     4921 aataacatca tttttgaaag aatagtattt tataactctt tctgccagac cgtatggaaa
     4981 tgtagcagga tgttttctgt tacgagatgg atttattttc cataggtttg tcttttcata
     5041 atcgtcgccg atttttgagt caaaaacatc ctctttgcta tgatggtttc ttatgttcca
     5101 atctattaat ttatcagttt tttttctgta aacaagaatg tactcagtta ctggtactgg
     5161 tttatattgc aacggattgc ggtcagctgc gaatcgacgg cctctaccta aagcccagcc
     5221 agctccttct ggtttaaccc aatgtatatc atctatgaat tcatagcctt cttctataaa
     5281 taacctgtgc aagtcaaaag gaacagctat tctttttgat gcttcattcc gtgacgccct
     5341 tcttattaaa acgggcgaga cattgatgac gaaaaaacga ccttcgctta aaactctatg
     5401 gcactctttt attactgaac gcaatagaga gaggtattca tcatatgtat gatattcgga
     5461 atactctggt ttggcattgt aatatggcgg tgatgtgaat actaagttca ctgattcatc
     5521 aggtaatttt ttcaaggtct ccgcgcagtt gccttgtagt aacatgttat ttaatggtga
     5581 ctttgatatg attttttttt ctttttttac cttttttggg gtatggacaa cctccattgc
     5641 tttcttaata agaaatggag acttcgaact tttcttataa tcaata
//
