LOCUS       CP076087                3609 bp    DNA     circular BCT 06-AUG-2021
DEFINITION  Salmonella enterica strain CFSAN057258 plasmid pCFSAN057258,
            complete sequence.
ACCESSION   CP076087
VERSION     CP076087.1
DBLINK      BioProject: PRJNA186035
            BioSample: SAMN06115853
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3609)
  AUTHORS   Hoffmann,M., Balkey,M. and Luo,Y.
  TITLE     Whole genome sequencing of cultured pathogen
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3609)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JUL-2018) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administraion, 5100 Paint Branch Pkwy,
            College Park, MD, USA
REFERENCE   3  (bases 1 to 3609)
  AUTHORS   Hoffmann,M., Balkey,M. and Luo,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-MAY-2021) CFSAN, US FDA, 5001 Campus Drive, College
            Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 305x
            Sequencing Technology             :: Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/28/2021 14:45:27
            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)                     :: 4,652
            CDSs (total)                      :: 4,528
            Genes (coding)                    :: 4,447
            CDSs (with protein)               :: 4,447
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 81
            CDSs (without protein)            :: 81
            Pseudo Genes (ambiguous residues) :: 0 of 81
            Pseudo Genes (frameshifted)       :: 33 of 81
            Pseudo Genes (incomplete)         :: 50 of 81
            Pseudo Genes (internal stop)      :: 19 of 81
            Pseudo Genes (multiple problems)  :: 18 of 81
            CRISPR Arrays                     :: 3
            ##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..3609
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="CFSAN057258"
                     /isolation_source="water"
                     /db_xref="taxon:28901"
                     /plasmid="pCFSAN057258"
                     /geo_loc_name="USA:MD"
                     /collection_date="2016-09-08"
                     /collected_by="FDA"
     gene            join(2547..3609,1..455)
                     /locus_tag="CIU49_023250"
     CDS             join(2547..3609,1..455)
                     /locus_tag="CIU49_023250"
                     /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="QWN71308.1"
                     /translation="MKKNIVRQVLESYCPCISSELAERIKRQNPSMSSDAIRKMISRST
                     DIGKLPFLRFSHNRRFIYLKDDFGSFKFWRALKKCMREANSAYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYESVLKNLLSAKILRSVYIDGIGDCVLINNNIANDISIFNM
                     ANCESFFDKPIFELIKAWLRNLGIVAFNQIKTKYDGENNPVVGSFEWDITAPSYVSPLA
                     EYSSDGLIPGFVVCDFALGFNRNEITTDAADTFIRKVQMTKSSRTNQRIMFVLFARRFE
                     KNAFNKLRSEGVLAITIANAFGNKVDESLARLSKVIQGTLSIERHPDELLQMVKDLESI
                     SGENGNLRGYIFELFVSSQICNFYGYGNVRINKEYKINGKHAEADVVLETNDDIYIVEC
                     KNVKTLPSMEVSLWMKTRVPIINSYYKSNNPDNKNIHHRLWVTGNIYPKDINRLDEFKC
                     NNKKIDVDYLFGQSLDDFFYQKKQVFNLYRKVISPDYKKGQIPDFDL"
                     /name="NERD domain-containing protein"
     gene            complement(1314..1508)
                     /locus_tag="CIU49_023255"
     CDS             complement(1314..1508)
                     /locus_tag="CIU49_023255"
                     /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="QWN71309.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1792..2115
                     /locus_tag="CIU49_023260"
     CDS             1792..2115
                     /locus_tag="CIU49_023260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QWN71310.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          1544..1783
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(751..1271)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.905"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          1793..2112
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="4.38e-62"
ORIGIN
        1 ttgtttcctc tcaaatttgt aatttctatg gttatggaaa tgttcgtatt aataaagaat
       61 ataaaataaa cggtaaacat gccgaagctg atgttgtatt ggaaactaac gatgatattt
      121 atatcgttga gtgcaaaaat gttaagactt taccttcgat ggaggttagt ctttggatga
      181 aaacaagagt gccaattata aattcctact acaaatcaaa taaccctgat aacaaaaata
      241 tacatcatcg tttgtgggtt acggggaata tatatcctaa agatataaac cgattggacg
      301 agtttaaatg taataataag aagattgatg ttgattattt atttggtcag tctttggatg
      361 attttttcta ccaaaaaaaa caagtgttta atttatatag gaaagtcatt tcgccagatt
      421 ataaaaaagg gcaaataccc gattttgact tatagaatga cgttttctag tctctgcatt
      481 tcttgacgat gacggcttga aaagcgtatc ttcctccatg aaacgaaaaa accacccggc
      541 aaggtggttt ttcgaaggtt agttaatcct ggcagattac ctaacctagg taactggctt
      601 cagcagagcg cagataccaa atcctgtcct ttaagtgtag ccgtagttgg ggcatcactt
      661 caagaactct gtagtacgga ccgcattatc atcgctctgc tattccagtt accagtggct
      721 gctgccagtg gcgataagtc gtgtcttttc gggttggact caagacgata gttaccggat
      781 aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg
      841 acctacaccg ggccgagata ccaacagcgt gagctatgag aaagcgccac gcttcccgaa
      901 gggagaaagg cggacaggta tccggtaaac ggcagggtcg gaacaggaga gcgcacgagg
      961 gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctgg
     1021 cttgagcgtc gatttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccacc
     1081 ggcgcggcct ttttcgggtt cttgtttttt gctcacatgt ttcttttggc tttatcccct
     1141 gattctgtgg ataaccgcat taccgtcttt gagtgagctg ataccgctcg ccgcagccga
     1201 acgaccgagc gtagcgagtc agtgagcgag gaagcggaag agcgccttat gtggcatttt
     1261 ctccttacgc accggtatac cgttctgcat cctgtctgga gcaggataca ctgttatacc
     1321 ccggtgccac tttccgcttc aaagcgtgtc tgtatgctgt tctggagttc ttccgcgagt
     1381 tcgtgcagct tctcacacat ggcggcctgt tcgtcggcat cgagtgcgtc cagcttttcg
     1441 agcagcgtca ggctctggct ttttatgaat cccgccatgt tgagtacggt ttgctgctgc
     1501 ttgttcatct tttcgttttc tccgttctgt ctgtcatctg cgttatgtga ttatatcgcg
     1561 taccactttt cgactgtttt gctgccgcta ttctgccgcc tggctttttg acgggcattt
     1621 ctgtcagaca acactgtcac tgccaaaaaa ctgccgtgcc tttgtcggta attcgagctt
     1681 gctgacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac
     1741 cctggtcagg gctttgcccc gacacccatg tcagatacgg agccatgttt tatgacaaaa
     1801 cgaagtggaa gtaatacgcg caggcgggct atcagtcgcc ctgttcgtct gacggcagaa
     1861 gaagaccagg aaatcagaaa aagggctgct gaatgcggca agaccgtttc cggtttttta
     1921 cgggcggcag ctctcggtaa gaaagttaac tcactgactg atgatcgggt actgaaagaa
     1981 gttatgagac tgggggcgtt acagaaaaaa ctctttatcg acggcaagcg tatcggggac
     2041 agggagtatg cggaggtgct gatcgctatt acggagtatc accgtgccct gttatccagg
     2101 cttatggcag attagcttcc cggggagaaa actgttgaaa acagacggta tgaacaccgt
     2161 aagctcccaa agtgatcacc attcgctttc atgcataact atgcagcgag ctgaaaacga
     2221 tcctgacgca tccttcctgt ttttccgggg taaaacatct ctttttgcgg tgtctgcgtc
     2281 agaatcgcgt tcagcgcgtt tcagtggtgc gtacaattaa gggattatgg taaatagggc
     2341 ggttgatata tgatgatgaa atgtcacaaa cgtaacatct tgatttttaa ggataaatct
     2401 cgcaggtgtg ttttttgtga tatgttgctt ttgttaaatg tttgattttt atgatttttt
     2461 tctttgtgtt tttttttggg atctatagat attacacgta gtgtaatttt ataaatagcg
     2521 tagtgtgaca aaaataagat gaatttatga aaaaaaacat tgttagacaa gtgcttgaga
     2581 gttattgtcc gtgcatatct tctgaacttg ctgagaggat taagcgtcag aatccttcta
     2641 tgtcatctga tgcaatacgt aaaatgatct ctcgaagcac tgatattggt aagttgccat
     2701 ttttaagatt tagtcataac aggagattca tttatctaaa agatgacttt ggtagcttca
     2761 aattttggcg ggcgctcaaa aaatgtatgc gtgaggcaaa ttcggcgtat tctcacgcta
     2821 tactttccgt aattaataat ggcggatact tgaaggtaaa ggatttcggg attgtgtctg
     2881 gctctccgat aaagcaggcc aagcatttaa gttatgaatc tgttctaaaa aatctgcttt
     2941 cagctaaaat acttagatct gtgtatattg atggtattgg tgattgtgtt ttgataaata
     3001 ataatatagc taatgatatc agcatcttta atatggcaaa ttgcgagtct ttttttgata
     3061 agccaatatt tgaactgatt aaggcatggt tgcgaaattt aggtattgtg gcttttaatc
     3121 aaataaaaac aaaatatgat ggagagaaca atcctgtggt tggttctttc gagtgggata
     3181 taacagcgcc aagttatgtg tcccctcttg ctgaatattc cagcgatgga ctcatcccag
     3241 gttttgttgt ctgtgatttt gctctagggt ttaatcgaaa tgaaattacc accgatgctg
     3301 ctgatacctt cataagaaaa gttcagatga ccaagtcctc taggacaaac cagaggatta
     3361 tgtttgttct ttttgctaga cgttttgaga agaatgcctt caacaagcta aggagtgaag
     3421 gggttctggc tataactata gctaatgcgt ttggtaataa ggtcgatgag agcttggcca
     3481 gactatcgaa ggtgattcag ggaactttat ctattgaaag acatcctgat gagttacttc
     3541 aaatggtaaa agatctggag tctatctctg gagagaatgg aaatttaagg gggtatattt
     3601 ttgagcttt
//
