LOCUS       NZ_CP063704             4888 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Enteritidis strain D7795
            plasmid pRGI00316, complete sequence.
ACCESSION   NZ_CP063704
VERSION     NZ_CP063704.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16552336
            Assembly: GCF_015240855.1
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 4888)
  AUTHORS   Perez Sepulveda,B.M., Predeus,A.V. and Hinton,J.C.D.
  TITLE     Four genomes of S. Enteritidis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4888)
  AUTHORS   Perez Sepulveda,B.M., Predeus,A.V. and Hinton,J.C.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-OCT-2020) Institute of Infection, Veterinary &
            Ecological Sciences, University of Liverpool, Crown St, Liverpool L7
            3EA, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2018
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Illumina HiSeq; PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:44:47
            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)                     :: 4,812
            CDSs (total)                      :: 4,691
            Genes (coding)                    :: 4,483
            CDSs (with protein)               :: 4,483
            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)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 88 of 208
            Pseudo Genes (incomplete)         :: 135 of 208
            Pseudo Genes (internal stop)      :: 39 of 208
            Pseudo Genes (multiple problems)  :: 47 of 208
            Pseudo Genes (short protein)      :: 1 of 208
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063704.1.
            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..4888
                     /organism="Salmonella enterica subsp. enterica serovar
                     Enteritidis"
                     /mol_type="genomic DNA"
                     /strain="D7795"
                     /serovar="Enteritidis"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149539"
                     /plasmid="pRGI00316"
                     /geo_loc_name="Malawi"
                     /lat_lon="13.2543 S 34.3015 E"
                     /collection_date="2000"
                     /collected_by="MLW"
     gene            complement(712..1143)
                     /locus_tag="IRO94_RS23870"
     CDS             complement(712..1143)
                     /locus_tag="IRO94_RS23870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_024249395.1"
                     /translation="MARVSISEAARLACVSRPTIYKLIKSGELSYTSVVKHGKAVKVID
                     TTELIRVFGSLSFDNERDHAVVKFDDRSTGVNSDFLQNLQHQVALLQAENAGLKDAVNA
                     RDEHINSLRQAMQLLEHKQGTADPQHVRAKSWWQFWKFR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1143..1334)
                     /locus_tag="IRO94_RS23875"
     CDS             complement(1143..1334)
                     /locus_tag="IRO94_RS23875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_021543809.1"
                     /translation="MTKPQKTALNMAKFIKGQTLLLLEKLNELELDAEADLCEKLHEDA
                     ELLCRTLTIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2583..3161
                     /locus_tag="IRO94_RS23880"
     CDS             2583..3161
                     /locus_tag="IRO94_RS23880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310049.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021543812.1"
                     /translation="MAKLPLPPLPLPIAPPSTVKNSGSERAKKSGRRTLAAKRKTLLEE
                     LWGDELEQLKVWNRHEHDGYTTVPRTLTYISRILDYLGGTGQPLSQTYLALWCRVFDEG
                     FVEIKDKDGFAYEAGFSGQRAVTTWTGRMRKLRDLGFITTKPGTSGEFQYVILLNPLTV
                     IKELYEGKEKDERYNALVGRMQEVGAKWE"
                     /name="hypothetical protein"
     gene            3165..3710
                     /locus_tag="IRO94_RS23885"
     CDS             3165..3710
                     /locus_tag="IRO94_RS23885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310050.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021543811.1"
                     /translation="MASYFPTLEISGKEFDFTHLEPFIMHVNSDMAKKVLKVHVRFTNH
                     CFTKGYEPFYHPEGEPIIYDHSENKRTFCPIRYRLSLALPEIIKRLCDPAEKVYQTSAK
                     RNWTYSITIDDPEGPYHLFFEIRRASRDERHLQDLNVVIESAYPEDRGYGPPSLLGRIG
                     FVGLCGRVFCGKPLATKR"
                     /name="hypothetical protein"
     Typing          97..352
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.154"
                     /coverage="99.0"
                     /evalue="3.2100000000000013e-72"
     Typing          complement(1710..1940)
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.966"
                     /coverage="91.0"
                     /evalue="6.509999999999999e-94"
ORIGIN
        1 atgtttaatt gtaataccgg cacacacaac gtattgccac ttggtcagag tttcccccac
       61 aacatcagtg cgaacgtgct taatgctcgc tacggctctc tcatgttgcc ggtgattccg
      121 ttgttgttct ttcaggaatg agtcatcaga tagccccaga aactcgctca aaagcactca
      181 gacgcgtgaa acgggtttta gatgcccgtc agggcatgga aggcgcgaat aacgcttaca
      241 gagcgtttca ggaggtcagg cgcgccgata cctaactagg ggatttcatg tcgctgggaa
      301 ccgagtcatc ccctgcaaag ccaattcgca cggaacagta agccactcgg ttggtagatg
      361 gtcgtagacc gtcagtgcta cagcaatggg ggtctcccca gacggtttcc tgttgcgctc
      421 aaggctctgc cggaaccgta gcggcaagga taaaaaaccc tgcgcacctt cccgcagggg
      481 aaggtgaaaa taactaccta tctcttacgt ttgagttttg aactcagact gaatatgcat
      541 ttgatagtgt tgaatttgca agaatcggcg gcgattttac ggtcgacaaa agagcaatgc
      601 aggaatatcg actccaactc aatgctctta atgtgggaaa atttccgttt tccaaattac
      661 cccaaactga gtggcagacc gaacgctatg gctgggatgc gtggtaatgg ctcaacggaa
      721 tttccaaaac tgccaccagg actttgctcg gacatgctgc ggatcagcag tgccctgctt
      781 atgctccagt agctgcatgg cctgacgaag tgaattgata tgttcgtccc gggcattcac
      841 tgcatctttc agcccggcgt tttctgcctg caaaagtgct acctgatgct gtaaattctg
      901 taaaaaatca ctgttaacac ctgtcgagcg gtcgtcaaat tttacaacag catggtcacg
      961 ttcattgtca aaagaaagag aaccaaaaac acgaataagc tctgtagtat caataacttt
     1021 tacagctttc ccatgcttta caacagaggt gtaacttaac tcaccagatt taattaactt
     1081 gtaaatagtc ggacgactga cacaagcaag gcgtgccgct tcgctaatag ataccctggc
     1141 cattatagat ccccctgatg accatccaga cgaatagtca gagtgcgaca gagtagttcc
     1201 gcatcctcat ggagcttttc gcaaaggtcc gcctcagcat cgagctcgag ttcattaagt
     1261 ttttccagca aaagcagggt ctgcccctta ataaacttcg ccatattaag cgcagttttc
     1321 tgtggtttcg tcatcacagc gtcagtgctc catgttaact ctggttcttt tccgcttcct
     1381 cgaccgttcg ctcgctacgc tcggtcactt gtctgcggcg agcggacggg gcttacggag
     1441 aagcaggtaa gagagtagat gatggacgta aggaaagggc agccaaaaag catgagaagg
     1501 ccacgccccc tgggcgtttt accataggct ccgcccccct gacgagcatc acagaatctg
     1561 acgctcaaat cagtggtggc gaaacccgac aggactataa agataccagg cgtttccccc
     1621 tggtggctcc ctcttgcgct ctcctgttcc cgccatgcgg cttacgtgtt gtggtggaag
     1681 ccttacctaa atcaccacgt cccgttccgt ttagacagtt cgctccaagc tgggctgtat
     1741 gcaagaaccc cccgttcagc ccgactacca cgttgtttcg gtaactatca tcttgagtcc
     1801 aacccggaac agacacgaaa aatcgccagt ggtggtagcc attggtaaac aggatgtgcg
     1861 agagatgtat cgagagttct tgaagtgatg gccttactcc ggctacactg aaaggacaga
     1921 tttggtgaca tgtctcgcac aagactgtta ccacggttag aaaatctgcc aggattaact
     1981 aaccttcgaa aaaccacctg ccagggtggt tttttcgttt acagagcaag agattacgcg
     2041 cagaaaaaaa ggatctcaag aagaaccttt ttatttcatg ctcactggta cgccccctcc
     2101 ccgtaaaact caaaacgctt aacgcagaat aatgtcaatt tccccaatca gcatccacac
     2161 attactctca cgtcgtctca gacacactca agcaagtgcc aaggccatcc cccccccccc
     2221 tctaatgccg gaaaaaatcg cacacagggc acagtgagca gccatttcgc ttcgtattaa
     2281 atagctgtcg aaaattatta ccttgccccc ttgcatcccc attcagcaca gcgagcacat
     2341 tcagcacata tcagcacatt cagtacagcg agcacagaaa ccagtcataa ctcattgaat
     2401 aaaggccacc atatgctgta tttattacaa ctcatacatc gagatgtaat aaatagatat
     2461 tcataagatg tctatagatt gataggcaac agcacaattg cacacaaaac aacatacaag
     2521 tcattgtttt aaaagaaaaa acaactaaaa taaccgcatg ttaaatgatt ttggagaata
     2581 taatggcgaa gctaccactg ccaccactgc cactaccaat agcgccaccg tcaacagtaa
     2641 aaaatagtgg ttcagaaaga gcgaagaagt caggaaggag aactcttgct gcaaaaagga
     2701 aaactttgtt agaagagcta tggggagacg agcttgaaca actcaaggta tggaatcgcc
     2761 atgaacatga cgggtataca acagtgccaa gaacgctgac atatatcagt cggatcctcg
     2821 attacctcgg aggtacgggc cagccattgt ctcaaacata tctggctctt tggtgcagag
     2881 tatttgatga aggatttgtg gaaataaagg ataaagatgg atttgcttat gaggctggtt
     2941 ttagcggaca gcgagctgta accacatgga cagggaggat gaggaaacta agagatttag
     3001 gtttcataac tacaaaacca ggcacatcag gtgagtttca atatgtaatt ttgcttaacc
     3061 cgctgactgt cattaaagag ttatacgaag gtaaagaaaa agatgaaagg tataacgcat
     3121 tggtgggacg tatgcaggag gttggcgcta aatgggagta attcatggct agctatttcc
     3181 caacgttaga aatatcagga aaagagttcg atttcacgca ccttgagcca ttcattatgc
     3241 acgtaaatag tgacatggct aaaaaggtat taaaagtaca tgtgagattc acaaatcatt
     3301 gtttcacaaa aggttatgag cctttttatc atccggaagg agaaccgata atttacgacc
     3361 atagcgagaa taagagaacg ttttgcccaa ttagatatag attatctttg gcgttacctg
     3421 agattatcaa acgtctatgt gatccagcag aaaaagtgta tcaaacatcg gcaaagagaa
     3481 actggaccta ctccattaca attgatgatc cggaagggcc atatcactta ttttttgaaa
     3541 taagacgcgc ctcacgtgat gagagacatc tgcaagattt gaatgttgtt atcgagagtg
     3601 cctatcctga agatcggggg tacgggcctc cgtcattact aggtcgaatt ggttttgtag
     3661 gcttatgcgg tagggtattt tgtgggaaac cacttgcgac taaaagatga aaaaaaagca
     3721 cctgaaaggt gccttttttt catctttggt aatcgttccg gacaccacta gcttttgctt
     3781 aggttcgcct tgcgcgaaca caggaacaag gtttgccctg ctgggtagcg ttcaatctca
     3841 tccggtcagt cgctacgatg taaacaatat aacaaaacca attacgcaat tcagcaccat
     3901 caattcaatg caacgcctca aatgatatag agcaccatga gtacaaaaac catagttaac
     3961 cgcatgaatt tacaaggcca tatgtatttt ataaaacaac tcagcattcg agttacttta
     4021 taaaatacat atggccttgt agcccatcat gattttgcta caacagaaaa aacatagtca
     4081 tttgttttta ttgaaaaaaa ttagacttct gtatctatcg tttttgatgt tttagcaatc
     4141 gttccgtatg gcttactgtg gctaaacatg ctgatgatta cacccagctt gttcaggtct
     4201 accgtttaca gctcatagcg ttcggagtat ttaccataac gtctcattac gcgcaccgca
     4261 gaaacgcgct gaacgcgatt ctgccgcaaa caccgcaaaa agagatgctt tatccagtga
     4321 aaaccagaaa aatgcgtcag gatcgttttc agctcgctgc atagctatgc atgagagtga
     4381 atggcgaacg gtttgggtgc atacagtgcc catgaggcac attttcagac attttcagtt
     4441 cgtgaattcc aagcattttt tacaggacac ccctaggggc gctgctaggg gtgtcctgta
     4501 aaaagatgcg acgcgcccct agggacgacc ctacattaat taactgtttt ttataaagat
     4561 tgtcagtact gaccctaagt agggtcgtca tagcatcgcc atagggtcat caacgacgtg
     4621 cttttgcata aatctgaaaa agaaaataca tttttaaaac aataacatca tgatttaaaa
     4681 agaaaatcag caaaaagtta gttttgcgtg gggtgtgggc atttcaggca tgagaacaga
     4741 ctcgcgtttt tccggggtat ctgcggaatt tttgattaaa aaaacatcga cgcagagcga
     4801 aattttatgc aacagcggct gtactgcaca gggattattt atcagttgat atgctgtgtc
     4861 atgatactac ctgaagaaac aggacagg
//
