LOCUS       NC_021816               3609 bp    DNA     circular CON 16-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str.
            CFSAN001921 plasmid unnamed3, complete sequence.
ACCESSION   NC_021816
VERSION     NC_021816.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN01832087
            Assembly: GCF_000430145.2
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str.
            CFSAN001921
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5- ...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3609)
  AUTHORS   Hoffmann,M., Muruvanda,T., Allard,M.W., Korlach,J., Roberts,R.J.,
            Timme,R., Payne,J., McDermott,P.F., Evans,P., Meng,J., Brown,E.W.
            and Zhao,S.
  TITLE     Complete Genome Sequence of a Multidrug-Resistant Salmonella
            enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken
            Breast
  JOURNAL   Genome Announc 1 (6), e01068-13 (2013)
   PUBMED   24356834
  REMARK    Erratum:[Genome Announc. 2014 Apr 03;2(2):e00294-14. doi:
            10.1128/genomeA.00294-14. PMID: 24699967] Publication Status:
            Online-Only
REFERENCE   2  (bases 1 to 3609)
  AUTHORS   Timme,R.E., Allard,M., Strain,E. and Brown,E.
  TITLE     Rapid genome closure with Pacific Biosystems technology
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 3609)
  AUTHORS   Strain,E.A., Allard,M.W., Payne,J. and Timme,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2013) 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                   :: SMRT Analysis v. 1.3.3
            Assembly Name                     :: CFSAN001921_01.0
            Genome Coverage                   :: 80x
            Sequencing Technology             :: PacBio RS
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000430145.2-RS_2024_06_16
            Annotation Date                   :: 06/16/2024 14:42:08
            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)                     :: 4,988
            CDSs (total)                      :: 4,866
            Genes (coding)                    :: 4,716
            CDSs (with protein)               :: 4,716
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 150
            CDSs (without protein)            :: 150
            Pseudo Genes (ambiguous residues) :: 0 of 150
            Pseudo Genes (frameshifted)       :: 54 of 150
            Pseudo Genes (incomplete)         :: 110 of 150
            Pseudo Genes (internal stop)      :: 23 of 150
            Pseudo Genes (multiple problems)  :: 32 of 150
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP006052.1.
            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..3609
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium var. 5- str. CFSAN001921"
                     /mol_type="genomic DNA"
                     /strain="CFSAN001921"
                     /serovar="Typhimurium var. 5-"
                     /isolate="11NY04CB01-S"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:1271862"
                     /plasmid="unnamed3"
                     /collection_date="03-Jul-1905"
     gene            complement(join(3334..3609,1..48))
                     /gene="mobA"
                     /locus_tag="CFSAN001921_RS24790"
     CDS             complement(join(3334..3609,1..48))
                     /gene="mobA"
                     /locus_tag="CFSAN001921_RS24790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_001699352.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            332..526
                     /locus_tag="CFSAN001921_RS24795"
                     /old_locus_tag="CFSAN001921_24860"
     CDS             332..526
                     /locus_tag="CFSAN001921_RS24795"
                     /old_locus_tag="CFSAN001921_24860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="WP_001041642.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1022..1180
                     /locus_tag="CFSAN001921_RS27960"
     CDS             1022..1180
                     /locus_tag="CFSAN001921_RS27960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071532985.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPKRHDLSPLAAATGNWNSRAMIM
                     RSVLQSS"
                     /name="replication initiation protein"
     gene            complement(1385..2902)
                     /locus_tag="CFSAN001921_RS24800"
                     /old_locus_tag="CFSAN001921_24865"
     CDS             complement(1385..2902)
                     /locus_tag="CFSAN001921_RS24800"
                     /old_locus_tag="CFSAN001921_24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000739598.1"
                     /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_020833675.1"
                     /translation="MKKNIVRQVLESYGPCISSELAERIKRQNPSMSSDAIRKMISRST
                     DIGKLPFLRFSHNRRFIYLKDDFGSFKFWRALKKCMREANSAYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYESVLKNLLSAKILRSVYIDGIGDCVLINNNIANDISIFNM
                     ANCESFFDKPIFELIKAWLRNLGIVAFNQIKTKYDGENNPVVGSFEWDITAPSYVSPLA
                     EYSSDGLIPGFVVCDFALGFNRNEITTDAADTFIRKVQMTKSSRTNQRIMFVLFARRFE
                     KNAFNKLRSEGVLAITIANAFGNKVDESLARLSKVIQGTLSIERHPDELLQMVKDLESI
                     SGENGNLRGYIFELFVSSQICNFYGYGNVRINKEYKINGKHAEADVVLETNDDIYIVEC
                     KNVKTLPSMEVSLWMKTRVPIINSYYKSNNPDNKNIHHRLWVTGNIYPKDINRLDEFKC
                     NNKKIDVDYLFGQSLDDFFYQKKQVFNLYRKVISPDYKKGQIPDFDL"
                     /name="NERD domain-containing protein"
     Typing          complement(58..297)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          570..1090
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.905"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(3338..3609)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.802"
                     /coverage="85.0"
                     /evalue="2.49e-51"
ORIGIN
        1 gcgactgata gcccgcctgc gcgtattact tccacttcgt tttgtcataa aacatggctc
       61 cgtatctgac atgggtgtcg gggcaaagcc ctgaccaggg taattgtaat agcgtgcatg
      121 tatgcgcggt ataacaattg cacatcctgt cctgtcagca agctcgaatt accgacaaag
      181 gcacggcagt tttttggcag tgacagtgtt gtctgacaga aatgcccgtc aaaaagccag
      241 gcggcagaat agcggcagca aaacagtcga aaagtggtac gcgatataat cacataacgc
      301 agatgacaga cagaacggag aaaacgaaaa gatgaacaag cagcagcaaa ccgtactcaa
      361 catggcggga ttcataaaaa gccagagcct gacgctgctc gaaaagctgg acgcactcga
      421 tgccgacgaa caggccgcca tgtgtgagaa gctgcacgaa ctcgcggaag aactccagaa
      481 cagcatacag acacgctttg aagcggaaag tggcaccggg gtataacagt gtatcctgct
      541 ccagacagga tgcagaacgg tataccggtg cgtaaggaga aaatgccaca taaggcgctc
      601 ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt cggctgcggc gagcggtatc
      661 agctcactca aagacggtaa tgcggttatc cacagaatca ggggataaag ccaaaagaaa
      721 catgtgagca aaaaacaaga acccgaaaaa ggccgcgccg gtggcgtttt tccataggct
      781 ccgcccccct gacgagcatc acaaaaatcg acgctcaagc cagaggtggc gaaacccgac
      841 aggactataa agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc
      901 gaccctgccg tttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc
      961 tcatagctca cgctgttggt atctcggccc ggtgtaggtc gttcgctcca agctgggctg
     1021 tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga
     1081 gtccaacccg aaaagacacg acttatcgcc actggcagca gccactggta actggaatag
     1141 cagagcgatg ataatgcggt ccgtactaca gagttcttga agtgatgccc caactacggc
     1201 tacacttaaa ggacaggatt tggtatctgc gctctgctga agccagttac ctaggttagg
     1261 taatctgcca ggattaacta accttcgaaa aaccaccttg ccgggtggtt ttttcgtttc
     1321 atggaggaag atacgctttt caagccgtca tcgtcaagaa atgcagagac tagaaaacgt
     1381 cattctataa gtcaaaatcg ggtatttgcc cttttttata atctggcgaa atgactttcc
     1441 tatataaatt aaacacttgt tttttttggt agaaaaaatc atccaaagac tgaccaaata
     1501 aataatcaac atcaatcttc ttattattac atttaaactc gtccaatcgg tttatatctt
     1561 taggatatat attccccgta acccacaaac gatgatgtat atttttgtta tcagggttat
     1621 ttgatttgta gtaggaattt ataattggca ctcttgtttt catccaaaga ctaacctcca
     1681 tcgaaggtaa agtcttaaca tttttgcact caacgatata aatatcatcg ttagtttcca
     1741 atacaacatc agcttcggca tgtttaccgt ttattttata ttctttatta atacgaacat
     1801 ttccataacc atagaaatta caaatttgag aggaaacaaa aagctcaaaa atataccccc
     1861 ttaaatttcc attctctcca gagatagact ccagatcttt taccatttga agtaactcat
     1921 caggatgtct ttcaatagat aaagttccct gaatcacctt cgatagtctg gccaagctct
     1981 catcgacctt attaccaaac gcattagcta tagttatagc cagaacccct tcactcctta
     2041 gcttgttgaa ggcattcttc tcaaaacgtc tagcaaaaag aacaaacata atcctctggt
     2101 ttgtcctaga ggacttggtc atctgaactt ttcttatgaa ggtatcagca gcatcggtgg
     2161 taatttcatt tcgattaaac cctagagcaa aatcacagac aacaaaacct gggatgagtc
     2221 catcgctgga atattcagca agaggggaca cataacttgg cgctgttata tcccactcga
     2281 aagaaccaac cacaggattg ttctctccat catattttgt ttttatttga ttaaaagcca
     2341 caatacctaa atttcgcaac catgccttaa tcagttcaaa tattggctta tcaaaaaaag
     2401 actcgcaatt tgccatatta aagatgctga tatcattagc tatattatta tttatcaaaa
     2461 cacaatcacc aataccatca atatacacag atctaagtat tttagctgaa agcagatttt
     2521 ttagaacaga ttcataactt aaatgcttgg cctgctttat cggagagcca gacacaatcc
     2581 cgaaatcctt taccttcaag tatccgccat tattaattac ggaaagtata gcgtgagaat
     2641 acgccgaatt tgcctcacgc atacattttt tgagcgcccg ccaaaatttg aagctaccaa
     2701 agtcatcttt tagataaatg aatctcctgt tatgactaaa tcttaaaaat ggcaacttac
     2761 caatatcagt gcttcgagag atcattttac gtattgcatc agatgacata gaaggattct
     2821 gacgcttaat cctctcagca agttcagaag atatgcacgg accataactc tcaagcactt
     2881 gtctaacaat gttttttttc ataaattcat cttatttttg tcacactacg ctatttataa
     2941 aattacacta cgtgtaatat ctatagatcc caaaaaaaaa cacaaagaaa aaaatcataa
     3001 aaatcaaaca tttaacaaaa gcaacatatc acaaaaaaca cacctgcgag atttatcctt
     3061 aaaaatcaag atgttacgtt tgtgacattt catcatcata tatcaaccgc cctatttacc
     3121 ataatccctt aattgtacgc accactgaaa cgcgctgaac gcgattctga cgcagacacc
     3181 gcaaaaagag atgttttacc ccggaaaaac aggaaggatg cgtcaggatc gttttcagct
     3241 cgctgcatag ttatgcatga aagcgaatgg tgatcacttt gggagcttac ggtgttcata
     3301 ccgtctgttt tcaacagttt tctccccggg aagctaatct gccataagcc tggataacag
     3361 ggcacggtga tactccgtaa tagcgatcag cacctccgca tactccctgt ccccgatacg
     3421 cttgccgtcg ataaagagtt ttttctgtaa cgcccccagt ctcataactt ctttcagtac
     3481 ccgatcatca gtcagtgagt taactttctt accgagagct gccgcccgta aaaaaccgga
     3541 aacggtcttg ccgcattcag cagccctttt tctgatttcc tggtcttctt ctgccgtcag
     3601 acgaacagg
//
