LOCUS       NZ_CP063292             5633 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Enteritidis strain
            R17.4111 plasmid pR17.4111_p5.6k, complete sequence.
ACCESSION   NZ_CP063292
VERSION     NZ_CP063292.1
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 5633)
  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  JOURNAL   Unpublished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 5633)
  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
            CP063292.1.
            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..5633
                     /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_p5.6k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST11"
     gene            join(4742..5633,1..869)
                     /locus_tag="IN817_RS23910"
                     /old_locus_tag="IN817_23910"
     CDS             join(4742..5633,1..869)
                     /locus_tag="IN817_RS23910"
                     /old_locus_tag="IN817_23910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AIPR family protein"
                     /protein_id="WP_057515538.1"
                     /translation="MARDDFNSDTRTVGLARLANSLEETYGSFINMENTNSKGEARREV
                     LITRCIAAHAVRMYGDELDPGVAAASVCDGSDDGGIDAVYVNPSSKKLILVQSKYIKDG
                     NGSVTIKDFGRFKDACAKVIANDLNSFNDRFLEHKESVTTAITSSSYKCICVFIYSGTQ
                     GLSSEVIGEIDFWEKSQNKALLFRDLESRDEYTILFETPNVTDISTSLSNQSTGAIDIS
                     NVILESYGEITEPYGAIYGTIAARVIHDWWKKYKYALFEKNIRSVLGDSTSVNAGIMST
                     IENSPENFWYYNNGITATYEEVDESIANAGASRKIGIFGFKKLNIINGAQTVSSIGAIF
                     DSIPEEKKDKARVMIRFINAKDPVFLGDVTKYNNTQNRVTGRDFTTQRPEQQKIQREIN
                     FVGGYTYKLLRQEDSGIAASNVIDIDDSLNALICESKKPQLIATLKSNRGRFFDTTEGN
                     LYEQVFNPRNPPSGISVINAVNLYRVCFDVLKDTITKASNSSEDEYSKIPSLLTHGNYV
                     FISILMGKIQPINTVNGIKTYDKNSVSFDTLELAKSIFEYIQSNYPNSYLARFFQNKEK
                     VEQIITHFSS"
                     /name="AIPR family protein"
     gene            1097..1423
                     /locus_tag="IN817_RS23915"
                     /old_locus_tag="IN817_23915"
     CDS             1097..1423
                     /locus_tag="IN817_RS23915"
                     /old_locus_tag="IN817_23915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /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_042927524.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRR
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDTLTPSERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1632..>2054
                     /locus_tag="IN817_RS23920"
                     /old_locus_tag="IN817_23920"
                     /pseudo=""
     CDS             1632..>2054
                     /locus_tag="IN817_RS23920"
                     /old_locus_tag="IN817_23920"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            2101..2586
                     /locus_tag="IN817_RS23925"
                     /old_locus_tag="IN817_23925"
     CDS             2101..2586
                     /locus_tag="IN817_RS23925"
                     /old_locus_tag="IN817_23925"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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_072035998.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMIRTSVSAAMAWVFLCFALLIGIMGGIIWFQGTIITSRLSEMD
                     SYSQQLANLKAKSGAGVAIYSDDKHRNTYMVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            2656..2880
                     /locus_tag="IN817_RS23930"
                     /old_locus_tag="IN817_23930"
     CDS             2656..2880
                     /locus_tag="IN817_RS23930"
                     /old_locus_tag="IN817_23930"
                     /inference="COORDINATES: protein motif:HMM:NF016769.3"
                     /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_226939304.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3042..3374
                     /locus_tag="IN817_RS23935"
                     /old_locus_tag="IN817_23935"
     CDS             3042..3374
                     /locus_tag="IN817_RS23935"
                     /old_locus_tag="IN817_23935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000017531.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKIRMATGNQGKSGSVRVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            3376..3660
                     /gene="nadS"
                     /locus_tag="IN817_RS23940"
                     /old_locus_tag="IN817_23940"
     CDS             3376..3660
                     /gene="nadS"
                     /locus_tag="IN817_RS23940"
                     /old_locus_tag="IN817_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            3853..4755
                     /locus_tag="IN817_RS23945"
                     /old_locus_tag="IN817_23945"
     CDS             3853..4755
                     /locus_tag="IN817_RS23945"
                     /old_locus_tag="IN817_23945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652796.1"
                     /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_057515539.1"
                     /translation="MNNAVLELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     SDKDIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYDQWLQACYERASAYNLQFPAPLD
                     EKEVNGIAKSIAKWTEKNFTASSFKEYVINSHRSDIQSKRGRLGGLKSKGGGRPTINSP
                     WEGMGISKSTYYRNIHGKR"
                     /name="replication initiation protein"
     Typing          1414..2978
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.743"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caacatatga agaggtagat gagagcatag ctaatgctgg agcatctcgg aaaattggaa
       61 tattcggatt taaaaagtta aacataataa atggggcgca aactgtaagc tctattgggg
      121 ctatatttga tagcataccc gaggagaaaa aagacaaagc tcgagtgatg attaggttta
      181 taaatgcgaa agatcctgtt tttttaggtg acgtaactaa gtacaacaat actcagaata
      241 gagttactgg cagagatttc acaacacaaa gacctgaaca gcaaaaaata cagagagaaa
      301 taaactttgt tgggggttat acatataagc tcttacgaca ggaagattca gggatagctg
      361 cttctaatgt tatcgatata gatgactcat taaatgcact aatttgcgaa tcaaagaaac
      421 ctcaacttat tgcaactttg aagtctaata gaggtcgttt ttttgataca acagagggca
      481 atctttacga acaagttttt aacccaagaa atccgccatc cggtatttct gttatcaatg
      541 ctgttaattt atacagagta tgtttcgatg ttttaaaaga tacaattact aaagcatcta
      601 actcatcaga agatgaatat agtaaaattc catcactgct gacgcatggt aactatgtat
      661 ttattagtat tttaatgggg aaaatacaac ccataaatac agttaatggc ataaaaacct
      721 atgacaagaa tagcgtctct tttgatactc ttgaactagc taaaagcata tttgaataca
      781 tccagtctaa ttatcctaac agctatctgg ctagattttt ccagaacaaa gaaaaagtag
      841 agcagatcat cactcacttt tcatcgtgag actaaacaag cctatatcag ataacagccc
      901 tctctagcag agggcttttt ttttgcagcc accacataat ctgatatcct gcaccttaca
      961 ctaagccagt acacacagcg tcccctctaa cgaggtgcca ctgtgactgg ttcagggggc
     1021 tcgccgcccc ccgaaacccc cggcatccac tgcgaaaaat tctcacagtg gtgcgaattt
     1081 tctctcagcg gagcctatgg aaaagcgaac gaaagagatc aaaatccggc tcaccgaaac
     1141 cgagcatcag cgactgcttg atcgctgcga ccggactcac cttgcggagt ggctgcgtca
     1201 gcttggtctg ggtgaacaca cttcacgcag gcgccgtgtg cccgatgtgg cgcccgaatt
     1261 gctgcgacag gtcagcggaa tcggtaacaa cctgaaccag attgcccgcc gtctgaacca
     1321 gactgacacc ctgacgccct ctgaacgtgc ttcgctgctt gtcgtactga ctagccttga
     1381 tcggcagctt ggcgacctgc tggagcagaa ccgtgatcgt taaaattcat tcgcggggtg
     1441 cgggttcggg cagcggtcct gtggattacc tgctgggaaa agaccggcag cgcgaacagg
     1501 ccagcgtact gcgcggcaat cctgaacatg tgcgtgagct gatcgacggc tgcaactttg
     1561 cccgcgccta cacttccggc gtgctttcat tccaggaacc tgacattgca gacgccgaga
     1621 aatcgcgcct gatggacgaa tgggagcaca cgctgctgac cggactcgac cgcgaccagt
     1681 acgcctgcct gtgggtagag catcgcgaca agggacggct tgagctgaat tttgtcatcc
     1741 cgaacatcga attgcagagt ggaaaacgcc tgcaacccta ctttgaccgc gccgaccgtc
     1801 cccgcgtcaa cgcctggcag accctgacca acgaccggct ggggctgcgc gacccgaatg
     1861 acccgaccta ccgccgtccg ctgacgcagg ccagcgatct gccccgcgac aaacagcagg
     1921 cggcagagaa aatcaccgcc ggcctgatga acctgatgca gcagggcgtg atccgcagcc
     1981 ggcaggacgt ggtgacgcag ctggaaagct acggcctgac cgtagcgcgg gaaacgaaaa
     2041 gtagcatcag cattgccgat ccggacggcg gccgaaatat ccggctgaaa ggaatgattt
     2101 atgagcgaga ttttaaattt ggcgaagggc ttcgaggaga aatcgaagca gcaggcgcag
     2161 gataccgagc agagcgtgaa gcgcgagttc gcgaggctgg agacgtctat cagcgcggaa
     2221 ctgcaatcaa gctcgcagag catcagcaac gctatccgcg agcagaacgg caggctgacg
     2281 ggcatgatca gaacctccgt ttcagcggcg atggcgtggg tattcctctg cttcgccctg
     2341 ctgatcggca tcatgggggg gataatctgg tttcagggta cgatcatcac ctcgcgcctg
     2401 agcgaaatgg acagctacag ccagcagctg gcgaacctga aagcgaaaag cggcgcgggc
     2461 gtggcgatct acagcgacga caagcaccgg aacacctaca tggtggtgct gccgaagcag
     2521 gcgcacggcg tggaaaccta tacatcgacg accgacaaca ccgtagtgaa atacacggcg
     2581 aaataacccc gtcagagcgc cctgaaacga cacagcgcgt ttttaacacc gaggatgacc
     2641 aaaaccatga ccgagatgga aaaacagctt ctgagcgcct tagagagctt acagacaagc
     2701 tacgagcaac agcagcaggc gtggcaggac agctacagca gcttgcagca catgttcgag
     2761 gctacctcac aggcgctgac gcacagcgac cgggtgtgtc agcacttgag cagtcaggta
     2821 gagagcttgc gcgcgcaggt cgagagcttg agcaggaacg tcagccgctt gatgcgttga
     2881 tcaggcagca cgaccgcgcc tacgccgaga agctgcgtga gcagcagcca gagccggagc
     2941 cgcagaaaaa aacgacccgc tactatggcc cctcgatgtg accgcttttc cgaaatcaga
     3001 attaagtgta ctatgtactc cgttaaaaac aggagacagc cgtgagtcac gcgattgagt
     3061 ttatcgagac cccgatgttt acccgtcaga taaaacagat cgccacggat gaagaactca
     3121 gggagctgca aaagacgctg attgagtcgc cggacaaagg cgatctcatt cagaaaaccg
     3181 gcgggctgcg caaaatcagg atggcgacgg gcaaccaggg aaaaagcggc agcgtgaggg
     3241 tgatttactt tctggccacc gccgaggtga tctatctggt gatggcctac ccgaaaagca
     3301 ccaaagacag cctgacggac gcggaaaaag ccgcgctgaa gacgctgacc caacaactga
     3361 aagacgaggt gtgacatgag tttttttgac gagctgaaag catcgctgga agaagccgtt
     3421 gaaatcaaaa acggcgtcag agagcctgcc cgcgtcaccc gttacgagct ggcagacgtg
     3481 aaagccatca gggcacagct gaacgtatct cagagcgaga tggcgaaagt gctgggaacc
     3541 agcctcgaca ccatcaagag ctgggaaacc ggacgccgta acccgaccgg actggcggcg
     3601 aaggtactgg caaccatcca ggcgaacccg aaattcttcc aggaactggc ggcgcactaa
     3661 gccgttgtga cagaaggatt agacaggcga ggccgttcgc gtgtaattta acggcaacag
     3721 aaaaaacaaa gccccggaaa tcatgctcaa tcttggcgga tgcacatgat aaccagggcc
     3781 aggtcgaaac cttgaaagga tattagcaca tgaaacgtgc cagacaacag cccgccataa
     3841 gcgcagggcg aattgaataa cgcagtactc gaacttttca acgaccgctt accgcacaag
     3901 ccgtacttct cggatgattt acactttggt gtacgcattg cagggaaaga acgcgccatt
     3961 ctggcgaaat acatccagtt caatcagcct cacgccatgt tctggctggg attcgacgtc
     4021 gatcgcgccg gtgccgccat cgactggagc gatcgcaacg cgcccgcgcc cacgctgacc
     4081 atcaccaacc cggaaaacgg acacgcgcac ctgctgtacg cgctggaaac ctcgatacgc
     4141 accgcacctg acgggaaaat gaagccgctg cgctacgccg ctgccgtgga gaatgcgcta
     4201 cgtaaaaaat tagaggctga tgcggggtat tcgggactaa tctgcaaaaa tccgaaccac
     4261 ggacactgga aaattgccgt atggcagccg gaactctaca cgctggactg gctggctgat
     4321 tttctcgacc tgaatgcagc gagcgacaaa gacatcgttg ctgactacgg cttaggccgt
     4381 aactgcaccc tgttcgacaa aacccgcaaa tgggcatacc gcgccatccg tcagggctgg
     4441 ccggagtatg accagtggct acaagcctgc tacgaacgcg caagtgctta caatctgcaa
     4501 ttccctgcac ctctggatga aaaagaggtg aatgggatag ctaaaagcat tgcaaaatgg
     4561 actgaaaaaa actttacagc atcttcattt aaagagtacg taattaactc tcatagaagc
     4621 gatattcaat ctaaaagagg tcgtttaggc ggattaaaaa gcaaaggtgg cggcaggcca
     4681 acaataaact ccccgtggga aggtatgggg attagtaaat cgacatatta caggaatatt
     4741 catggcaaga gatgatttta atagcgacac tagaaccgtt gggcttgcaa ggttagctaa
     4801 tagcctagaa gaaacctatg gttcttttat taatatggaa aacactaact ctaaaggtga
     4861 ggctagaaga gaagttctga tcacaagatg cattgctgcg catgcagtaa ggatgtatgg
     4921 tgatgaactc gaccctggag ttgctgctgc atcagtttgc gatggtagcg atgatggggg
     4981 aattgatgct gtttatgtaa acccaagttc taaaaaactt attttggtac agtcaaaata
     5041 tataaaagat gggaatggtt ctgtaacaat aaaagatttt ggacggttta aagacgcatg
     5101 tgcaaaagtt atagctaacg atctcaattc atttaatgat agatttttag agcacaaaga
     5161 atcagtgact acggctatca ctagtagtag ctataaatgc atatgcgttt ttatttattc
     5221 aggaacccaa gggttaagct cagaagtgat tggagagatt gatttttggg agaaaagcca
     5281 aaacaaagcg ctgttgttta gagatttaga atctagggat gagtatacaa tactatttga
     5341 aacgcctaat gttactgaca tatctactag cttgagcaat caatctaccg gagctataga
     5401 tataagtaat gtaatattag agtcgtatgg tgagatcact gaaccttacg gcgcaatcta
     5461 cggaacgatt gctgcaaggg tgatacatga ttggtggaaa aaatacaagt atgcgctttt
     5521 cgagaaaaat ataagaagtg tcttgggtga ttcgacatca gtaaatgcag ggatcatgtc
     5581 taccatcgaa aatagcccag agaacttttg gtactataac aacgggatta ctg
//
