LOCUS       NZ_CP063293             3610 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Enteritidis strain
            R17.4111 plasmid pR17.4111_p3.6k, complete sequence.
ACCESSION   NZ_CP063293
VERSION     NZ_CP063293.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16450742
            Assembly: GCF_015074885.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella
            enteritidis)
  ORGANISM  Salmonella enterica subsp. enterica serovar Enteritidis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3610)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Salmonella enterica subsp. enterica serovar Enteritidis strain
            R17.4111
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3610)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 16-OCT-2020
            Assembly Method                   :: Unicycler v. v0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:55:57
            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)                     :: 4,823
            CDSs (total)                      :: 4,702
            Genes (coding)                    :: 4,517
            CDSs (with protein)               :: 4,517
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 185
            CDSs (without protein)            :: 185
            Pseudo Genes (ambiguous residues) :: 0 of 185
            Pseudo Genes (frameshifted)       :: 74 of 185
            Pseudo Genes (incomplete)         :: 124 of 185
            Pseudo Genes (internal stop)      :: 39 of 185
            Pseudo Genes (multiple problems)  :: 46 of 185
            Pseudo Genes (short protein)      :: 1 of 185
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063293.1.
            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..3610
                     /organism="Salmonella enterica subsp. enterica serovar
                     Enteritidis"
                     /mol_type="genomic DNA"
                     /strain="R17.4111"
                     /serovar="Enteritidis"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149539"
                     /plasmid="pR17.4111_p3.6k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST11"
     gene            complement(31..1548)
                     /locus_tag="IN817_RS23950"
                     /old_locus_tag="IN817_23950"
     CDS             complement(31..1548)
                     /locus_tag="IN817_RS23950"
                     /old_locus_tag="IN817_23950"
                     /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"
     gene            complement(1981..2304)
                     /gene="mobA"
                     /locus_tag="IN817_RS23955"
                     /old_locus_tag="IN817_23955"
     CDS             complement(1981..2304)
                     /gene="mobA"
                     /locus_tag="IN817_RS23955"
                     /old_locus_tag="IN817_23955"
                     /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            2588..2782
                     /locus_tag="IN817_RS23960"
                     /old_locus_tag="IN817_23960"
     CDS             2588..2782
                     /locus_tag="IN817_RS23960"
                     /old_locus_tag="IN817_23960"
                     /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            3278..3436
                     /locus_tag="IN817_RS24265"
     CDS             3278..3436
                     /locus_tag="IN817_RS24265"
                     /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"
     Typing          complement(2314..2553)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          2826..3346
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.905"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(1985..2304)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="4.38e-62"
ORIGIN
        1 caagaaatgc agagactaga aaacgtcatt ctataagtca aaatcgggta tttgcccttt
       61 tttataatct ggcgaaatga ctttcctata taaattaaac acttgttttt tttggtagaa
      121 aaaatcatcc aaagactgac caaataaata atcaacatca atcttcttat tattacattt
      181 aaactcgtcc aatcggttta tatctttagg atatatattc cccgtaaccc acaaacgatg
      241 atgtatattt ttgttatcag ggttatttga tttgtagtag gaatttataa ttggcactct
      301 tgttttcatc caaagactaa cctccatcga aggtaaagtc ttaacatttt tgcactcaac
      361 gatataaata tcatcgttag tttccaatac aacatcagct tcggcatgtt taccgtttat
      421 tttatattct ttattaatac gaacatttcc ataaccatag aaattacaaa tttgagagga
      481 aacaaaaagc tcaaaaatat acccccttaa atttccattc tctccagaga tagactccag
      541 atcttttacc atttgaagta actcatcagg atgtctttca atagataaag ttccctgaat
      601 caccttcgat agtctggcca agctctcatc gaccttatta ccaaacgcat tagctatagt
      661 tatagccaga accccttcac tccttagctt gttgaaggca ttcttctcaa aacgtctagc
      721 aaaaagaaca aacataatcc tctggtttgt cctagaggac ttggtcatct gaacttttct
      781 tatgaaggta tcagcagcat cggtggtaat ttcatttcga ttaaacccta gagcaaaatc
      841 acagacaaca aaacctggga tgagtccatc gctggaatat tcagcaagag gggacacata
      901 acttggcgct gttatatccc actcgaaaga accaaccaca ggattgttct ctccatcata
      961 ttttgttttt atttgattaa aagccacaat acctaaattt cgcaaccatg ccttaatcag
     1021 ttcaaatatt ggcttatcaa aaaaagactc gcaatttgcc atattaaaga tgctgatatc
     1081 attagctata ttattattta tcaaaacaca atcaccaata ccatcaatat acacagatct
     1141 aagtatttta gctgaaagca gattttttag aacagattca taacttaaat gcttggcctg
     1201 ctttatcgga gagccagaca caatcccgaa atcctttacc ttcaagtatc cgccattatt
     1261 aattacggaa agtatagcgt gagaatacgc cgaatttgcc tcacgcatac attttttgag
     1321 cgcccgccaa aatttgaagc taccaaagtc atcttttaga taaatgaatc tcctgttatg
     1381 actaaatctt aaaaatggca acttaccaat atcagtgctt cgagagatca ttttacgtat
     1441 tgcatcagat gacatagaag gattctgacg cttaatcctc tcagcaagtt cagaagatat
     1501 gcacggacca taactctcaa gcacttgtct aacaatgttt tttttcataa attcatctta
     1561 tttttgtcac actacgctat ttataaaatt acactacgtg taatatctat agatcccaaa
     1621 aaaaaaacac aaagaaaaaa atcataaaaa tcaaacattt aacaaaagca acatatcaca
     1681 aaaaacacac ctgcgagatt tatccttaaa aatcaagatg ttacgtttgt gacatttcat
     1741 catcatatat caaccgccct atttaccata atcccttaat tgtacgcacc actgaaacgc
     1801 gctgaacgcg attctgacgc agacaccgca aaaagagatg ttttaccccg gaaaaatagg
     1861 aaggatgcgt caggatcgtt ttcagctcgc tgcatagtta tgcatgaaag cgaatggtga
     1921 tcactttggg agcttacggt gttcataccg tctgttttca acagttttct ccccgggaag
     1981 ctaatctgcc ataagcctgg ataacagggc acggtgatac tccgtaatag cgatcagcac
     2041 ctccgcatac tccctgtccc cgatacgctt gccgtcgata aagagttttt tctgtaacgc
     2101 ccccagtctc ataacttctt tcagtacccg atcatcagtc agtgagttaa ctttcttacc
     2161 gagagctgcc gcccgtaaaa aaccggaaac ggtcttgccg cattcagcag ccctttttct
     2221 gatttcctgg tcttcttctg ccgtcagacg aacagggcga ctgatagccc gcctgcgcgt
     2281 attacttcca cttcgttttg tcataaaaca tggctccgta tctgacatgg gtgtcggggc
     2341 aaagccctga ccagggtaat tgtaatagcg tgcatgtatg cgcggtataa caattgcaca
     2401 tcctgtcctg tcagcaagct cgaattaccg acaaaggcac ggcagttttt tggcagtgac
     2461 agtgttgtct gacagaaatg cccgtcaaaa agccaggcgg cagaatagcg gcagcaaaac
     2521 agtcgaaaag tggtacgcga tataatcaca taacgcagat gacagacaga acggagaaaa
     2581 cgaaaagatg aacaagcagc agcaaaccgt actcaacatg gcgggattca taaaaagcca
     2641 gagcctgacg ctgctcgaaa agctggacgc actcgatgcc gacgaacagg ccgccatgtg
     2701 tgagaagctg cacgaactcg cggaagaact ccagaacagc atacagacac gctttgaagc
     2761 ggaaagtggc accggggtat aacagtgtat cctgctccag acaggatgca gaacggtata
     2821 ccggtgcgta aggagaaaat gccacataag gcgctcttcc gcttcctcgc tcactgactc
     2881 gctacgctcg gtcgttcggc tgcggcgagc ggtatcagct cactcaaaga cggtaatgcg
     2941 gttatccaca gaatcagggg ataaagccaa aagaaacatg tgagcaaaaa acaagaaccc
     3001 gaaaaaggcc gcgccggtgg cgtttttcca taggctccgc ccccctgacg agcatcacaa
     3061 aaatcgacgc tcaagccaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt
     3121 tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgttta ccggatacct
     3181 gtccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct gttggtatct
     3241 cggcccggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc
     3301 cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccgaaaa gacacgactt
     3361 atcgccactg gcagcagcca ctggtaactg gaatagcaga gcgatgataa tgcggtccgt
     3421 actacagagt tcttgaagtg atgccccaac tacggctaca cttaaaggac aggatttggt
     3481 atctgcgctc tgctgaagcc agttacctag gttaggtaat ctgccaggat taactaacct
     3541 tcgaaaaacc accttgccgg gtggtttttt cgtttcatgg aggaagatac gcttttcaag
     3601 ccgtcatcgt
//
