LOCUS       NZ_CP009568             3605 bp    DNA     circular CON 08-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Newport str. CVM 22462
            plasmid pCFSAN000934_03, complete sequence.
ACCESSION   NZ_CP009568
VERSION     NZ_CP009568.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN01813482
            Assembly: GCF_000272895.2
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Newport str. CVM 22462
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport str. CVM 22462
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3605)
  AUTHORS   Cao,G., Allard,M.W., Hoffmann,M., Monday,S.R., Muruvanda,T., Luo,Y.,
            Payne,J., Rump,L., Meng,K., Zhao,S., McDermott,P.F., Brown,E.W. and
            Meng,J.
  TITLE     Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant
            Salmonella enterica subsp. enterica Serotype Newport
  JOURNAL   Genome Announc 3 (1), e00027-15 (2015)
   PUBMED   25720681
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3605)
  AUTHORS   Timme,R., Allard,M.W., Strain,E., Evans,P.S. and Brown,E.
  TITLE     Whole genome shotgun sequencing of cultured foodborne pathogen
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 3605)
  AUTHORS   Strain,E.A., Allard,M.W., Payne,J.S., Evans,P.S., Timme,R. and
            Cao,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-SEP-2014) Center for Food Safety and Applied
            Nutrition, United States Food and Drug Administration, 5100 Paint
            Branch Parkway, College Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRTPortal HGAP v. 2.1.2
            Assembly Name                     :: CFSAN000934.0
            Genome Coverage                   :: 100X
            Sequencing Technology             :: PacBio RS II
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/08/2023 04:49:43
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,078
            CDSs (total)                      :: 4,955
            Genes (coding)                    :: 4,817
            CDSs (with protein)               :: 4,817
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 138
            CDSs (without protein)            :: 138
            Pseudo Genes (ambiguous residues) :: 0 of 138
            Pseudo Genes (frameshifted)       :: 54 of 138
            Pseudo Genes (incomplete)         :: 101 of 138
            Pseudo Genes (internal stop)      :: 21 of 138
            Pseudo Genes (multiple problems)  :: 34 of 138
            Pseudo Genes (short protein)      :: 1 of 138
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP009568.1.
            Bacterial culture available from Dwayne Roberson, FDA College Park
            Campus, 5100 Paint Branch Parkway, College Park, MD 20740.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3605
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport str. CVM 22462"
                     /mol_type="genomic DNA"
                     /strain="CVM 22462"
                     /serovar="Newport"
                     /isolation_source="Dog"
                     /host="Canis lupus familiaris"
                     /sub_species="enterica"
                     /db_xref="taxon:858305"
                     /plasmid="pCFSAN000934_03"
                     /geo_loc_name="USA: AZ"
                     /collection_date="2003"
                     /collected_by="CVM"
     gene            complement(621..770)
                     /locus_tag="SEEN462_RS28055"
     CDS             complement(621..770)
                     /locus_tag="SEEN462_RS28055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138881.1"
                     /translation="MPSEYDEQRDATDTQLPGEYDLFDLMAKVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            1329..1487
                     /locus_tag="SEEN462_RS28475"
                     /old_locus_tag="SEEN462_01575"
     CDS             1329..1487
                     /locus_tag="SEEN462_RS28475"
                     /old_locus_tag="SEEN462_01575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001403044.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKTPLAAAIGIWFTERRGV
                     YKHTQSS"
                     /name="hypothetical protein"
     gene            complement(1676..3208)
                     /locus_tag="SEEN462_RS01455"
                     /old_locus_tag="SEEN462_01580"
     CDS             complement(1676..3208)
                     /locus_tag="SEEN462_RS01455"
                     /old_locus_tag="SEEN462_01580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017899153.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NERD domain-containing protein"
                     /protein_id="WP_000750321.1"
                     /translation="MKKSVVRQVLEMSGPCISSDLAERIQWQYPSMSPEAIRKMISRST
                     DIGKLPFLKFSHNRRFIYLKDDFGSFKFWRALEKCMYEANSTYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYETVLRNLLSAKILRAVYIDGVGDCVLINNNIANDVNIRTM
                     ANCESFFDKPIFELVKAWLRNLGLVAFNQIKTKYDGEGNPVVGSFEWDMTAPSYVSPLA
                     EYVGGKLMPGFVACDFSLGFNRDEITTAAAETFIRKVQMTKSSRASQRIMFVIFARRFG
                     KIAFNKLRSEGVLAVTIANAFGNKVDESLTRLSRVVQGSLSIEKHPDELLQMVKDLESV
                     SGENGNLRGYVFELFVSSQISNFYGLGNIYINREYKINGKHAEADVVLESSDDIYIIEC
                     KNVKVLPSTELTRWMKERVPIINSYYKINNLEKKNIHHYLWVTGNVYNKDLKRLDSFKN
                     NNKNIDVDYLFGEHLDDFFYKKKRVFNLYRKVISPDYKKGVMPDFELEDDFF"
                     /name="NERD domain-containing protein"
     Typing          complement(764..979)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.845"
                     /coverage="100.0"
                     /evalue="7.43e-58"
     Typing          1148..1628
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.344"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 cgtgcagcca gtggaagtcc tgttttcgac gttcttctca tccgaaaacg gtgaacgggg
       61 acgcaattta ttgcgtgacc gtaaagcgtt ggcaagagca tcaagcatga agagaagggg
      121 gtcggatgta cgaatggttc agagaactgt tatgacgtaa ttcagtagta attcagtagt
      181 aaatcagtag tagataagta gtcatcctcc tccgatttgt agtaaatcag tagtaaatca
      241 gtagtgtttc tgtagtcccc cccctccggt ttgtagtaaa tcagtagtaa atcagtagtg
      301 acgctgtagt ttattagtag tcaggaggaa taagctgttc atacaagtat gaacgagcta
      361 gttatggacg ctttttttca cagatctcct cagaataggc aaagctcagc ccggtaagga
      421 gatgattctt tatcccttaa atggccatac accatacgca accgcgattt tcatcgcaat
      481 tgcatgaatt aaaaggtaaa aactgaagtt cccgtttatt tatgtaatac gcaacgtatt
      541 acaaccacct gtaatcacat gaaaataaag aaataagatg taataccggc gtattacacg
      601 tacgcgggta agcgaaaaag ctataacgct tcccggccga caggcggccc aaaatccacc
      661 ggggcgtgca ggttctcttc agtaaccttc gccattaaat caaaaaggtc atattcgccg
      721 ggaagctgcg tatcagtcgc atcccgttgt tcatcatatt cagatggcat ggggtgatat
      781 ccagtagcta aggggttgtt agcgggtttc ggagcgcagc cctgaaccag tcacgtagcg
      841 ctagcggagt ctaaactagc tgaatatgtt acggcggggt cggggttcag gaaagtgctt
      901 catgtgacag gggaaaatgc agctacaggg cgtacgggag aaaatggggg ttactgtgat
      961 atgacgcctc ctcgctcact cggtcgctac cgctcctgcc gttcggctgc ggcgggcgtt
     1021 agctgcacac ggataagagc aaaagcatgt ggcatgacaa acagggcagg aaaaggacgc
     1081 ggcgctgccg tttttccata ggctccgccc ccctgacaag catcacgaaa tctgacactc
     1141 aaatcagtgg tggcgaaacc cgacaggact ataaagatcc caggcgtttc cccctggtag
     1201 ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcactc cgctgttatg
     1261 gccgcgttta tctcattcca cgcctgacac tcagttccgg gaaggcagtt cgctccaagc
     1321 tggactgtat gcacgaaccc cccgttcagt ccgactgctg cgcctgttcc ggtaactatc
     1381 gacttgagtc caacccggaa agacacgaca aaacgccact ggcagcagcc attggtatct
     1441 ggtttacgga gcggagaggc gtgtacaagc atacacagag ttcttgaagt gttgacctga
     1501 ctacggctac actggaagga cagatttggt cactgcgctc cgtttaagcc agttaccacg
     1561 gttcagaaac ttgccggttt cctgaacctt cgaaaaacca ccttgccggg tggttttttc
     1621 gtttcagaga tggaagatac gcctttcaaa gcgccatcgt caagaaacgc agtagctaga
     1681 aaaaatcgtc ctctaactca aaatcaggca ttacgccttt tttataatca ggtgaaatga
     1741 cttttctata taagttgaac acccgctttt tcttgtaaaa gaaatcatcc aaatgctcac
     1801 caaacaaata atcaacatcg atattcttat tattattctt aaaagagtct aaccttttta
     1861 aatctttgtt gtacacattc cctgtaaccc acaaataatg gtggatattc tttttttcta
     1921 aattatttat tttatagtaa gagtttataa ttggaaccct ttctttcatc caacgcgtaa
     1981 gttcagttga aggtaagacc ttaacatttt tgcactctat tatataaata tcgtcactac
     2041 tctccaatac aacatcagct tctgcatgct taccatttat cttatactct ctattaatgt
     2101 aaatattacc aaggccataa aaattagaaa tttgcgagga tacaaaaagc tcaaaaacat
     2161 accctctcaa attgccattc tctccagaaa cagactccag atctttaacc atctgaagca
     2221 actcatctgg atgcttttca atggacaaag aaccctgaac caccctcgac aacctggtta
     2281 agctttcatc aactttatta ccaaacgcat ttgctatagt tacagccaga accccctcac
     2341 ttctcaactt attgaaggct attttgccga aacgccttgc gaaaataaca aacattatcc
     2401 tctgactcgc tcgagaagac ttggtcatct ggacttttct tatgaatgtt tctgctgcag
     2461 cggtagtaat ttcatcacga ttaaagccga gagaaaaatc acaggcaacg aaaccaggca
     2521 tcagttttcc gccgacatat tcagcgagag gggaaacgta acttggagcg gtcatatccc
     2581 attcaaaaga gcctacaact ggatttccct ccccatcata ttttgttttt atctgattaa
     2641 aagcgactag gcctaaattc ctcaaccaag ctttaacaag ctcaaatatt ggtttgtcaa
     2701 aaaaggattc gcaatttgcc attgttctaa tattaacatc gttggctatg ttgttattta
     2761 tcagtacgca atcaccaact ccatcaatat acacggctct aagtattttt gccgaaagta
     2821 gatttcttag aactgtttca taacttaaat gtttagcttg ttttatagga gatccagaca
     2881 caatcccaaa atctttcacc ttcaaataac cgccattatt tattacggaa agtatcgcgt
     2941 gtgagtaagt tgagtttgct tcgtacatgc acttttcgag agctcgccaa aatttgaaac
     3001 tgccaaaatc atcttttaga taaatgaatc tcctgttatg gctgaatttc aaaaatggca
     3061 gcttacctat gtccgtgctt cgcgagatca ttttacgtat cgcttcaggg gacattgagg
     3121 gatattgcca ctgaattctc tctgcaagat ccgaagagat gcatggcccg ctcatttcaa
     3181 gcacctgtct aacaacactt tttttcatat cctcacctta tttctgtcac actacgctat
     3241 ttataatatt acactacgtg taatagggcg cagtctttta aaaaaaagtg actataaaaa
     3301 ataattaaaa atcagatggt taattactta ctttaaattg agcacaaaga aatatcgtct
     3361 ttataattat ttaatccttt taaatcataa agatagtatt gtgacatttt tttatcgaac
     3421 tatcagctac tccatttacc ataacatccg ttgcgtgcac cgcctgagag gctctcaggg
     3481 cgtttctgac gggaaaccgg taaaacaagg caacaaacca cccgaaaacc agccagaaac
     3541 gcgcaggctc tgtttttacg gcatgcatga gtatgcgcgc aagtgcatag cgcagaattt
     3601 cacgc
//
