LOCUS       NC_021843               4675 bp    DNA     circular CON 16-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str.
            CFSAN001921 plasmid unnamed2, complete sequence.
ACCESSION   NC_021843
VERSION     NC_021843.1
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 4675)
  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 4675)
  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  JOURNAL   Unpublished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 4675)
  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
            CP006051.1.
            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..4675
                     /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="unnamed2"
                     /collection_date="03-Jul-1905"
     gene            complement(join(4671..4675,1..301))
                     /locus_tag="CFSAN001921_RS24760"
     CDS             complement(join(4671..4675,1..301))
                     /locus_tag="CFSAN001921_RS24760"
                     /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="WP_038406202.1"
                     /translation="MSQQYTVSIAPMAYQCLADIESYKSGYIGSLKAGDLVDNLLQESV
                     ACIIQDPERYHYNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDF"
                     /name="hypothetical protein"
     gene            complement(316..585)
                     /locus_tag="CFSAN001921_RS24765"
                     /old_locus_tag="CFSAN001921_24835"
     CDS             complement(316..585)
                     /locus_tag="CFSAN001921_RS24765"
                     /old_locus_tag="CFSAN001921_24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019080654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024143071.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            complement(888..1070)
                     /locus_tag="CFSAN001921_RS24770"
                     /old_locus_tag="CFSAN001921_24840"
     CDS             complement(888..1070)
                     /locus_tag="CFSAN001921_RS24770"
                     /old_locus_tag="CFSAN001921_24840"
                     /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="WP_020833677.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            complement(1167..1376)
                     /locus_tag="CFSAN001921_RS27420"
     CDS             complement(1167..1376)
                     /locus_tag="CFSAN001921_RS27420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014538403.1"
                     /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="WP_014538403.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1380..1865)
                     /locus_tag="CFSAN001921_RS27425"
     CDS             complement(1380..1865)
                     /locus_tag="CFSAN001921_RS27425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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="WP_024143073.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<1900..2553)
                     /locus_tag="CFSAN001921_RS27955"
                     /pseudo=""
     CDS             complement(<1900..2553)
                     /locus_tag="CFSAN001921_RS27955"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     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            complement(2543..2866)
                     /locus_tag="CFSAN001921_RS24780"
                     /old_locus_tag="CFSAN001921_24850"
     CDS             complement(2543..2866)
                     /locus_tag="CFSAN001921_RS24780"
                     /old_locus_tag="CFSAN001921_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="WP_024143074.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3949..4536
                     /locus_tag="CFSAN001921_RS24785"
                     /old_locus_tag="CFSAN001921_24855"
     CDS             3949..4536
                     /locus_tag="CFSAN001921_RS24785"
                     /old_locus_tag="CFSAN001921_24855"
                     /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="WP_020833680.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     Typing          complement(2976..3155)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          3135..3617
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.164"
                     /coverage="93.0"
                     /evalue="2.1e-176"
     Typing          complement(1058..2553)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatcctgctt catgctcaca aacaacagta tttcgatgtt cgttccgtca aaatcgtaaa
       61 gcaccctgta ttcactctca acatcgagcc gctcacgtaa aagcatacct cgatcctgta
      121 agtggaaatt gtagtgataa cgttcagggt cttggataat gcaggcaact gattcctgaa
      181 gtaagttatc aaccagatca ccggccttga gtgacccaat gtatccactc ttgtaagact
      241 cgatatcagc taaacattga tatgccatcg gcgcgattga aaccgtgtat tgctgggaca
      301 ctaaacacct ctctgttatt ttctagcggc acgcaacctc cctaagacct cttctggggt
      361 catgcctttg ccttctgtga tttccttttt agccaacgtt gccagcttaa aaagggcgtt
      421 gatattgcgt tcttctctca tctcacgaac ttcagcatca cgttctgctg cggtttggat
      481 gaataactca gctactccgt ttttagtgac gtaaacacct ccttcaaagg tttgtgcatt
      541 tccgagactg tctcttgcga gtttctggga catggtctgg ttcataggca tttttttctc
      601 atcatatagg ggcgcttccg gcgagaacgg cgctgcacga ttcaagggtc atagtttccg
      661 gtttgtggtt tcaggtttca ggtttcaggt ttcagtgttg atttattagg ccagtacaaa
      721 ttctcgctat ggcacatggt ggccagtgtc cgtgctttga atagagttta tcagttggtg
      781 tataaattga gtacatattt ttacacagaa aggtgaaaga agggaaaatt agtttaattc
      841 agaatcattt accataacat ctcttaccgg caccgctccg gacgggttca gcgcgaatgc
      901 gccgtcagcc cggaaaaaaa tacagttaac tccccggtaa aacgcgccgc ctgcgcctga
      961 taaatttcac ccgaatgcat agccatgcag acaggtgaat ggcaccggct ttcgccgcag
     1021 atattcgccg aaagccccgt tttatccggt ttgttacagc gacggtccat tgtacgtccg
     1081 ctgccgctgc gatcgttcaa gctccagcgt tttctggtgc tgcaccgccc gctcatgctc
     1141 ccggtgtgct tcaatgccgt ctagtctcac gacaaccggc gaagctgctc gctcaaactc
     1201 tgcacctgcc tgctcaagcc cgtgacgcgc tcgctcagcg ccgcgttctc ccgttgcata
     1261 agaccagaca tcgtccgcca ttccgcgaag gcgttctccc actcgtccag ccttttcgag
     1321 tagtcctgct gtagctgctc taatgcgctc agcagctgtt tttccagctc cgtcatgtgc
     1381 tatttccccg ccagtatcat ccagctcgaa tcctctccga acccgcccgc ttccgggttc
     1441 accctcacgc agcggcgtct ctgctctccg caggtcgtga gctgcacacc gctgttcctc
     1501 tctgacagca tggcctgcgt gttcttctgc tcccggatgg tcgtgtagtt ctcgagtatc
     1561 tgctgcccct gccaccacag aatgcccgcg ctcgaggcga tcagcagcgc ggagaccagc
     1621 acgatggtca gccacgtctg gctgaccatg cgcagcatcc ctttcgtgcg ctggctcatg
     1681 gctgaggaca gcttccggtc gtggtcgagg atggcggcgc tgattctctt ctcgctttcg
     1741 ctcagttccg ctctgacaga cttctcgtgc tcgctgaatg cggctttcag catctcgccg
     1801 gtagtctgct gctgcgcttt cgatttctgc tctaagtcct tcgccagcgt taaaagactg
     1861 ttcatagatg gctcccttca gtcggatgtt tcgccccccg tccgggtcgg caatgctgat
     1921 gctgcttttt gtggtgcgca ccacctcaaa acctgcgttt tccagcgcct cagtgacgtc
     1981 ctgtcgcgtt ttcagctccc cggacgaggc taaggccagt aaaccccgcg taatagtctg
     2041 ggcagcttcc tgcttcgttt ccggcagcgc ggacggcgtg gccagcgccc gccggttctc
     2101 cggcgcgttc gggtcgtgca gccccagccg accgttcacg atggtctgcc aggcatcgat
     2161 gcgcggacgg tcggcgcggt cgtaatacgg ctggagacgc ctgccggtca gcagctccgt
     2221 gtttggtatc aggaaattca gctcaagccg ccctttgtcg ttgtgctcaa cccacagcac
     2281 gctgtactga tctttatcga gtccgggcat cagaacccgc tcgaagctcg ccatcagctt
     2341 ttcacgctgt ccgggcggta agtcctgttc ggcaaatgac aggacgccgg aggtgtactt
     2401 tttggcgtaa ggcgaggcat cgataagctc ccggacttcc tccggcttcc cctgcagaac
     2461 gctggcgccg tcgcggtgcc ggtctttgcc cagcagataa tccaccggac cggcaccgcc
     2521 gccgcgccct ctcgggtgaa acttaacgat catcgtctgc ccctttttcc agtacggcgt
     2581 gccgcagccg ctcgagtcct gcgtcgatgg ccatcagcgc agcgacaacc tgcacgcggt
     2641 cgtgcccgct gccgccaccg gcgttaacct gccgggcaat ctggttgagg ttgtttccca
     2701 tgccggcaag ctgacgaagc agcgccggcg agatcgaggg aagtttgccg gcgcgggcgg
     2761 gcttctcgtc caggcacgtc tggcgcatcc aggccgcgag ctgtttaccc tcgcagcgct
     2821 ccagcagacg cctgtgctca tcttccgtca cccacatcgt gagcattttg ctgcgtttat
     2881 ctgccaatcc ggcctcctga taacgccggg acgggcggga aattctttcc cgggcggcgc
     2941 ggtgttgggc aagccgcagg cgcgtcagtg gcttttagcg ggtttcgggg cgcagccctg
     3001 aaccagtcac gtagcgctag cggagtgtat actggcttaa tatagtaaat cgaagtggga
     3061 attcagggaa gtgcttcatg tgacagagga aaaatgcggc tgtggggcgt aagtgcagaa
     3121 tgtaggtaaa agtgaaatga cgcctcctcg ctcactcggt cgctgcgctc ctgccgtgag
     3181 actgcggcgg gcgttacagg ctcacggata acgagataaa gcggaaggcg acacatcaga
     3241 aaggaacaga aaaaggatgc ggcgttgccg tttttccata ggctccgccc ccctgacgag
     3301 catcacgaaa tctgacgctc aaatcagtgg cggcgaaacc cgacaggact ataaagatcc
     3361 caggcgtttc cccctggtag ctccctcatg cgctctcctg ttcctgcctt tcggtttacc
     3421 ggtgtcattc cgctgttatg gccgcggttt ctcattccac gcctgacact cagttccggg
     3481 taggcagttc gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgaccgctgc
     3541 gccttatccg gtaactatca tcttgagtcc aacccggaaa gacacgactt atcgccactg
     3601 gcagcagcca ttggtaagag gatgtacaag agattactaa cgcagagttc ttgaagtatc
     3661 agcccaacta cggctaaact ggaaggacga atttggtggc agcggtcttg tacaccctgt
     3721 taccacggtt cagaagttcc ccaacttact gaaccatcga aaaaccacct ccccaggtgg
     3781 ttttttcgtt tctgggtcaa gagattacga ctcccacccg agaatctcaa gaagatcctt
     3841 caactctgtg ttcaaaacac tgtttaaaac agctataagc cttcaagata gtttcagaaa
     3901 tacaatgcta tttcactctc tggaaaacaa accaaaaagg tcaaaaaaat gataagaaag
     3961 attttttttg cttctgcaat cgtaatagcc atctctggct gtacagcaat ggataaattg
     4021 gcaggaatgg gtgttgtttc tcagcaaaca tcaacctttg ataactcgac cgttatagag
     4081 gtatctccaa attcgctata cgatcctaac agcacttggg gaacacaact tcagttgggc
     4141 gcgatatggt ctagtgccta tccagaagag gttgggctaa ttctttccta caactcgaat
     4201 gtatctagcg gaaatgccgc atacttaggt ttgacgggga ttgatataaa tattgatggc
     4261 aaaatatcca gctataaagc acagcagcaa actaatctaa gcagtagcgc atataactcc
     4321 gtatctaaaa cgatctatac ctctagcaag aacactgttg ttatccccta taaattgctg
     4381 gagagcatgg tatcagctaa aaactgccgc attcgcatac acacaagcca aggaaatcaa
     4441 gacatcgact tctcggcgca aagcatccct ggaggtaaag cgacagcgat cgtttccatt
     4501 aaagagttca tggtcaaagt cgaaagtttt aaataaggac acgtaagccc acctatatct
     4561 actaacttag tgttaatagg cataggtgga aatttttgtc tgcacgaaaa aacccgacga
     4621 tgccgggtgt ttagtgttaa ttcagcaaat tatagcgata cagctgcttt tcaaa
//
