LOCUS       NC_011079               3605 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Newport str. SL254
            plasmid pSL254_3, complete sequence.
ACCESSION   NC_011079
VERSION     NC_011079.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02604062
            Assembly: GCF_000016045.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Newport str. SL254
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport str. SL254
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3605)
  AUTHORS   Fricke,W.F., Mammel,M.K., McDermott,P.F., Tartera,C., White,D.G.,
            Leclerc,J.E., Ravel,J. and Cebula,T.A.
  TITLE     Comparative genomics of 28 Salmonella enterica isolates: evidence
            for CRISPR-mediated adaptive sublineage evolution
  JOURNAL   J Bacteriol 193 (14), 3556-3568 (2011)
   PUBMED   21602358
REFERENCE   2  (bases 1 to 3605)
  AUTHORS   Ravel,J., Fricke,W.F., White,D., McDermott,P., Mammel,M.,
            Rosovitz,M., Leclerc,J., Cebula,T. and Sebastian,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUL-2008) J. Craig Venter Institute, 9704 Medical
            Center Drive, Rockville, MD 20850, USA
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000016045.1-RS_2024_05_08
            Annotation Date                   :: 05/08/2024 01:30:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,916
            CDSs (total)                      :: 4,795
            Genes (coding)                    :: 4,674
            CDSs (with protein)               :: 4,674
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 47 of 121
            Pseudo Genes (incomplete)         :: 90 of 121
            Pseudo Genes (internal stop)      :: 20 of 121
            Pseudo Genes (multiple problems)  :: 32 of 121
            Pseudo Genes (short protein)      :: 1 of 121
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP001112.1.
            The sequenced strain has been deposited at the Salmonella Genetic
            Stock Centre at the University of Calgary under the care of Dr.
            K.E. Sanderson.
            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. SL254"
                     /mol_type="genomic DNA"
                     /strain="SL254"
                     /serovar="Newport"
                     /sub_species="enterica"
                     /db_xref="taxon:423368"
                     /plasmid="pSL254_3"
     gene            744..2276
                     /locus_tag="SNSL254_RS00995"
                     /old_locus_tag="SNSL254_B0002"
     CDS             744..2276
                     /locus_tag="SNSL254_RS00995"
                     /old_locus_tag="SNSL254_B0002"
                     /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"
     gene            complement(2465..2623)
                     /locus_tag="SNSL254_RS27300"
     CDS             complement(2465..2623)
                     /locus_tag="SNSL254_RS27300"
                     /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            3182..3331
                     /locus_tag="SNSL254_RS26885"
                     /old_locus_tag="SNSL254_B0005"
     CDS             3182..3331
                     /locus_tag="SNSL254_RS26885"
                     /old_locus_tag="SNSL254_B0005"
                     /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"
     Typing          2974..3189
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.845"
                     /coverage="100.0"
                     /evalue="7.43e-58"
     Typing          complement(2325..2805)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.344"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtatgaac agcttattcc tcctgactac taataaacta cagcgtcact actgatttac
       61 tactgattta ctacaaaccg gagggggggg actacagaaa cactactgat ttactactga
      121 tttactacaa atcggaggag gatgactact tatctactac tgatttacta ctgaattact
      181 actgaattac gtcataacag ttctctgaac cattcgtaca tccgaccccc ttctcttcat
      241 gcttgatgct cttgccaacg ctttacggtc acgcaataaa ttgcgtcccc gttcaccgtt
      301 ttcggatgag aagaacgtcg aaaacaggac ttccactggc tgcacggcgt gaaattctgc
      361 gctatgcact tgcgcgcata ctcatgcatg ccgtaaaaac agagcctgcg cgtttctggc
      421 tggttttcgg gtggtttgtt gccttgtttt accggtttcc cgtcagaaac gccctgagag
      481 cctctcaggc ggtgcacgca acggatgtta tggtaaatgg agtagctgat agttcgataa
      541 aaaaatgtca caatactatc tttatgattt aaaaggatta aataattata aagacgatat
      601 ttctttgtgc tcaatttaaa gtaagtaatt aaccatctga tttttaatta ttttttatag
      661 tcactttttt ttaaaagact gcgccctatt acacgtagtg taatattata aatagcgtag
      721 tgtgacagaa ataaggtgag gatatgaaaa aaagtgttgt tagacaggtg cttgaaatga
      781 gcgggccatg catctcttcg gatcttgcag agagaattca gtggcaatat ccctcaatgt
      841 cccctgaagc gatacgtaaa atgatctcgc gaagcacgga cataggtaag ctgccatttt
      901 tgaaattcag ccataacagg agattcattt atctaaaaga tgattttggc agtttcaaat
      961 tttggcgagc tctcgaaaag tgcatgtacg aagcaaactc aacttactca cacgcgatac
     1021 tttccgtaat aaataatggc ggttatttga aggtgaaaga ttttgggatt gtgtctggat
     1081 ctcctataaa acaagctaaa catttaagtt atgaaacagt tctaagaaat ctactttcgg
     1141 caaaaatact tagagccgtg tatattgatg gagttggtga ttgcgtactg ataaataaca
     1201 acatagccaa cgatgttaat attagaacaa tggcaaattg cgaatccttt tttgacaaac
     1261 caatatttga gcttgttaaa gcttggttga ggaatttagg cctagtcgct tttaatcaga
     1321 taaaaacaaa atatgatggg gagggaaatc cagttgtagg ctcttttgaa tgggatatga
     1381 ccgctccaag ttacgtttcc cctctcgctg aatatgtcgg cggaaaactg atgcctggtt
     1441 tcgttgcctg tgatttttct ctcggcttta atcgtgatga aattactacc gctgcagcag
     1501 aaacattcat aagaaaagtc cagatgacca agtcttctcg agcgagtcag aggataatgt
     1561 ttgttatttt cgcaaggcgt ttcggcaaaa tagccttcaa taagttgaga agtgaggggg
     1621 ttctggctgt aactatagca aatgcgtttg gtaataaagt tgatgaaagc ttaaccaggt
     1681 tgtcgagggt ggttcagggt tctttgtcca ttgaaaagca tccagatgag ttgcttcaga
     1741 tggttaaaga tctggagtct gtttctggag agaatggcaa tttgagaggg tatgtttttg
     1801 agctttttgt atcctcgcaa atttctaatt tttatggcct tggtaatatt tacattaata
     1861 gagagtataa gataaatggt aagcatgcag aagctgatgt tgtattggag agtagtgacg
     1921 atatttatat aatagagtgc aaaaatgtta aggtcttacc ttcaactgaa cttacgcgtt
     1981 ggatgaaaga aagggttcca attataaact cttactataa aataaataat ttagaaaaaa
     2041 agaatatcca ccattatttg tgggttacag ggaatgtgta caacaaagat ttaaaaaggt
     2101 tagactcttt taagaataat aataagaata tcgatgttga ttatttgttt ggtgagcatt
     2161 tggatgattt cttttacaag aaaaagcggg tgttcaactt atatagaaaa gtcatttcac
     2221 ctgattataa aaaaggcgta atgcctgatt ttgagttaga ggacgatttt ttctagctac
     2281 tgcgtttctt gacgatggcg ctttgaaagg cgtatcttcc atctctgaaa cgaaaaaacc
     2341 acccggcaag gtggtttttc gaaggttcag gaaaccggca agtttctgaa ccgtggtaac
     2401 tggcttaaac ggagcgcagt gaccaaatct gtccttccag tgtagccgta gtcaggtcaa
     2461 cacttcaaga actctgtgta tgcttgtaca cgcctctccg ctccgtaaac cagataccaa
     2521 tggctgctgc cagtggcgtt ttgtcgtgtc tttccgggtt ggactcaagt cgatagttac
     2581 cggaacaggc gcagcagtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc
     2641 gaactgcctt cccggaactg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc
     2701 ggagtgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga gctaccaggg
     2761 ggaaacgcct gggatcttta tagtcctgtc gggtttcgcc accactgatt tgagtgtcag
     2821 atttcgtgat gcttgtcagg ggggcggagc ctatggaaaa acggcagcgc cgcgtccttt
     2881 tcctgccctg tttgtcatgc cacatgcttt tgctcttatc cgtgtgcagc taacgcccgc
     2941 cgcagccgaa cggcaggagc ggtagcgacc gagtgagcga ggaggcgtca tatcacagta
     3001 acccccattt tctcccgtac gccctgtagc tgcattttcc cctgtcacat gaagcacttt
     3061 cctgaacccc gaccccgccg taacatattc agctagttta gactccgcta gcgctacgtg
     3121 actggttcag ggctgcgctc cgaaacccgc taacaacccc ttagctactg gatatcaccc
     3181 catgccatct gaatatgatg aacaacggga tgcgactgat acgcagcttc ccggcgaata
     3241 tgaccttttt gatttaatgg cgaaggttac tgaagagaac ctgcacgccc cggtggattt
     3301 tgggccgcct gtcggccggg aagcgttata gctttttcgc ttacccgcgt acgtgtaata
     3361 cgccggtatt acatcttatt tctttatttt catgtgatta caggtggttg taatacgttg
     3421 cgtattacat aaataaacgg gaacttcagt ttttaccttt taattcatgc aattgcgatg
     3481 aaaatcgcgg ttgcgtatgg tgtatggcca tttaagggat aaagaatcat ctccttaccg
     3541 ggctgagctt tgcctattct gaggagatct gtgaaaaaaa gcgtccataa ctagctcgtt
     3601 catac
//
