LOCUS       CP082557                4936 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            CVM N18S1602 plasmid pN18S1602-3, complete sequence.
ACCESSION   CP082557
VERSION     CP082557.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12360201
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Schwarzengrund
  ORGANISM  Salmonella enterica subsp. enterica serovar Schwarzengrund
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4936)
  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 4936)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUL-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4936)
  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                   :: 367x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:10:22
            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)                     :: 4,630
            CDSs (total)                      :: 4,510
            Genes (coding)                    :: 4,414
            CDSs (with protein)               :: 4,414
            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)              :: 96
            CDSs (without protein)            :: 96
            Pseudo Genes (ambiguous residues) :: 0 of 96
            Pseudo Genes (frameshifted)       :: 49 of 96
            Pseudo Genes (incomplete)         :: 52 of 96
            Pseudo Genes (internal stop)      :: 18 of 96
            Pseudo Genes (multiple problems)  :: 21 of 96
            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..4936
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S1602"
                     /serovar="Schwarzengrund"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="pN18S1602-3"
                     /geo_loc_name="USA:TN"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            join(4680..4936,1..454)
                     /locus_tag="FQD73_023120"
                     /pseudo=""
     CDS             join(4680..4936,1..454)
                     /locus_tag="FQD73_023120"
                     /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            432..950
                     /locus_tag="FQD73_023125"
     CDS             432..950
                     /locus_tag="FQD73_023125"
                     /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="UAI38516.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKDAIALFTTSTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQDGRRKFLVLPYGKSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            957..1190
                     /locus_tag="FQD73_023130"
     CDS             957..1190
                     /locus_tag="FQD73_023130"
                     /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="UAI38517.1"
                     /translation="MTELETHLLNALKQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSGQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1801..2097)
                     /locus_tag="FQD73_023135"
     CDS             complement(1801..2097)
                     /locus_tag="FQD73_023135"
                     /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="UAI38518.1"
                     /translation="MERKHKGKCPFCNSEMAPEVIEKNTIRRDKCKCTTCGEIIYKCRN
                     IFCNDYAKGGLLYDDELCPPCGEGLLKAVKEFPDKYRAAIQKVVEEKNREKNN"
                     /name="hypothetical protein"
     gene            complement(2172..2327)
                     /locus_tag="FQD73_023140"
     CDS             complement(2172..2327)
                     /locus_tag="FQD73_023140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010940654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1508 domain-containing protein"
                     /protein_id="UAI38519.1"
                     /translation="MNDKWEFYLDNSKEWRWRRTASNGRIVGASSQGYVNKSDCIDNAR
                     RHGYNG"
                     /name="DUF1508 domain-containing protein"
     gene            complement(4111..4302)
                     /locus_tag="FQD73_023145"
     CDS             complement(4111..4302)
                     /locus_tag="FQD73_023145"
                     /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="UAI38514.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4367..4690
                     /locus_tag="FQD73_023150"
     CDS             4367..4690
                     /locus_tag="FQD73_023150"
                     /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="UAI38515.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          3949..4033
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          complement(3381..3938)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1288
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.639"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4335..4687
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.22"
                     /coverage="100.0"
                     /evalue="5.1e-65"
ORIGIN
        1 aaaaaatcag tacagcatcc tgtgggtgga gcaccaggac aagggacggc ttgagctgaa
       61 ttttgtcatt ccgaacatgg agctacagac cggaaaacgc ctccagccgt actacgaccg
      121 ggcagacagg ccgagaattg atgcctggca gacgctggtt aatcaccatt acgggctgca
      181 tgaccccaac gccccggaga atcgccggac gctgacactc cctgataacc tgccggaaac
      241 gaaacaggcg cttgctgaga gcgttacacg aggcctggag gtgctttacc attccggaga
      301 gataaaaggc cgtcaggatg tgattcaggc gctcacagag gtggggcttg aagtggtcag
      361 ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaggaata tcagactgaa
      421 aggagcgttt tatgagcaat cttttacgga cgggcgcgga gttcgagaaa aagctgaaag
      481 agagagccga atctacagag aaaatgctga acgacgaatt cagcaggctc ggcgaatctg
      541 taagcgaggc tgtgacctca aacgagacga aaatcaaaga cgctatagcc ctgttcacaa
      601 cgtcgacaga ggaatcgctg aaaaaacacc gggaaggggt gaaagaggcg atgatgcagc
      661 accggaagga catgttaaag ctggcaggga gttcgggcat gaggttgctg gggatagtct
      721 ttctcctgtt taccgcgagt ggcgggacgc tctggtatct cggcgggagg atacagacga
      781 acctggaaga aatcagggta caggaagaga cattgcggaa actgaacgcg aagacatggg
      841 gcgtggagtt tgttcaggac gggagaagga aatttctggt ccttccgtac gggaaatcag
      901 cagaggtgac tcactatcag gggaaggact ggatacaact gacggagtga tacggaatga
      961 cagagctgga aacacatttg ctgaacgcct taaagcagct gcaacaggac tatatgcagc
     1021 ggctgaacga atgggagagc gccttcgtgg aattgcagaa gatgttttcg cttacgcaac
     1081 gggacaacgc gatgctgaac gagcgggtca tgcagttgag tcagcaggtg caacacttga
     1141 gcgggcagac agaacgcttg agccagttat acagcgagaa caggagataa gggatgaacg
     1201 gctgatgcag gagcgcgaac atgcattatc cctggagcgg gaacgccagc tggaaataca
     1261 ggaacgcaca ctggatggtc cttcgttgtc gctgtgatgg cgaaactatg aaaaatggca
     1321 ggttcggtgg attttgacgg gctaatgtgg tctgcaccat ctggttgcat aggtattcat
     1381 acggttaaaa tttatcaggc gcgatcgcgg cagtttttcg ggtggtttgt tgccattttt
     1441 acctgtctgc tgccgtgatc gcgatgaacg cgttttagcg gtgcgtacaa ttacagggtt
     1501 atgttaaatt gatggtttga taagtgttgg aaataattaa ttccactcat aaatatacaa
     1561 gatatgaaaa aaatattgtt catatggtag aagagctata gggatatttg gtttcaaaat
     1621 attcctttta ggaaatggat taactaaaac aggtactaaa atacctgtta aaaataatga
     1681 gagagataac tctctgttag ggcgtgtgtt ggggatatag aaatatttgg tattgcttac
     1741 gaaatcgatt ggttttcatg ataattaact aatatagtta tatggttttg tgcgctacca
     1801 ttaattattc ttttctctat tcttctcttc tacaactttt tgaattgctg ctcgatactt
     1861 atcagggaac tcttttaccg cctttaaaag accttcacca catggagggc acagttcgtc
     1921 atcgtaaagt aatccgcctt ttgcgtagtc attacagaat atatttcggc atttataaat
     1981 aatctctcca caagttgtac atttacattt atctctgcgg atagtgtttt tttctataac
     2041 ttctggagcc atttcgctat tgcaaaaagg gcacttacct ttgtgttttc tttccatggt
     2101 atttttctat ttgtttatct ctttgcaatt gggattcctg cttggaatcc caacatgaga
     2161 atcaatttat attagccgtt gtagccatga cgacgtgcgt tatcaataca atcagattta
     2221 ttgacatatc cttgagatga tgctccaaca attcgcccgt tgcttgcagt tctgcgccag
     2281 cgccactctt ttgaattatc gagataaaac tcccacttat cgttcattta ggtttccttc
     2341 ttccagttag atatttagtg atgatttgta ccagcaggta ggtatcattt catttttttt
     2401 tctaataagc gtgttacaac tgtactgacg acgatactta aggctgttgt ccctaatgcg
     2461 ccgatacttc tacctatgtt cgacatgcat gacgggcata attcatcatc atataaatga
     2521 ccgcccttag cgtaattctc acatcctgga gtacgacata cgtaaattat tgatttacaa
     2581 tcagaacact cacacttatc tcgccgtatc ttgttttctt gaattacacg ggcattgatt
     2641 tcctttttac aaaaaggaca cactccttta ggttttaagt ccattagggt ttacctaata
     2701 gcactacaac ttattaattt tgaacgacat ttagggcaat aatcaggtgt cccaaatcca
     2761 gctctactgg tccattcgtg gcggcagttt aagcatttag cccgatagat gacgatacct
     2821 gccataaaaa tccccttttt atcatacact aatgttgatt tattatattc tgaacataat
     2881 aaatgtaaag tatactatgt gataaacgta atgcattgat tttattgata ttaaaaatat
     2941 ttattagagt gctaataatg gtattttttt tgattttttt attaaaaaca atatgttgta
     3001 tatgtgttgg tgtcgtttga ttacgttcaa taaatgcgtg tatcaatatt agatatacaa
     3061 aaatgaagtt agaaggtggc tgggagtttt aggagatttg ccctccttca gtaaaaagat
     3121 caaaggatcc tcttgagatc ctttttttct gcgcgtaatc tgctgcctgt aaacgaaaaa
     3181 accgcctggg gaggcggttt agtcgaaggt taagtcagtt ggggactgct taaccgggta
     3241 actggcttgg tggagcacag ataccaaata ctgtccttct agtgtagccg cagttaggcc
     3301 accacttcaa gaactcttaa tatctcaatc caccttgtcc agttaccagt ggctgctgcc
     3361 agtggcgtta aggcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg
     3421 cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg aacgacctac
     3481 accgaactga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga
     3541 aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt
     3601 ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct ctgacttgag
     3661 cgtcgatttc tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcggcgtg
     3721 gccttttccg ggttcttgtt ttttgctcac atgtttcctt tggcgttatc ccctgattct
     3781 gtggataacc gcattaccgt ctttgagtga gctgataccg ctcgccgcag ccgaacgacc
     3841 gagcgtagcg agtcagtgag cgaggaagcg gaaaagcgcc tggacgcgca ttttctcctt
     3901 acgcatctgt gcggcatttc acacccggca tggggcactt ttcatacaat ctgcactgat
     3961 gccacatagt taagccagta tacactccgc tagcgctacg tgactggttc agggcttcgc
     4021 cccgaaaccc cctgacgcgc cctgacgggc ttgtctgctc ccggcatccg ctcacagaca
     4081 agctgtgacc gtctccggga gctgtatgtg tcagaggttt tcaccgtcat ccccgaagcg
     4141 tgcgaggcag ctgcggtaaa gctcgtcggc gtggtcgtga agtgattcac aaatatcggc
     4201 ctgttcatct gcgtccagtt cgttgagttt ctccagcagc gttaatgtct ggcttctgat
     4261 aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct ccgtgtaagg
     4321 gggatttctg ttcatggggg taatgatacc gatgaaacga gagaggatgc tcacgatacg
     4381 ggttactgat gatgaacatg cccggttact ggaacgctgt gagggtaaac aactggcggt
     4441 atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaagc tgccaacttt
     4501 ggctccgccg ttactgcgtc agctggccgc catcgggaat aacctgaatc agacagcgag
     4561 gaaggtgaac agcgggcagt ggtcttccgg cgaccgggtt caggtggtgg ccgcactgat
     4621 ggccatcgag agagagttgc gcagcttacg gcaggtcgtc agggaacagg gagcgcggga
     4681 tgatagttaa gtttcatgcc aggggaaaag gtggtggcag tggtccggtt gattacctgc
     4741 tggggaggga gcgtaatcgc gaaggcgcaa cggtgcttca gggtaatccg gaagaagtcc
     4801 gggaactcat cgatgccacg ccatttgcga agaaatacac gtccggtgtt ctgtcgtttg
     4861 cggagaaaga actgccaccg ggaggacgtg aaaaagtgat ggcgagtttt gagcgtgtac
     4921 tgatgcccgg tctcga
//
