LOCUS       NZ_CP063710             3272 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Enteritidis strain A1636
            plasmid pSE-GC, complete sequence.
ACCESSION   NZ_CP063710
VERSION     NZ_CP063710.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16552338
            Assembly: GCF_015241115.1
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 3272)
  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  JOURNAL   Unpublished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 3272)
  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                   :: 12/13/2023 03:23:43
            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)                     :: 4,641
            CDSs (total)                      :: 4,520
            Genes (coding)                    :: 4,348
            CDSs (with protein)               :: 4,348
            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)              :: 172
            CDSs (without protein)            :: 172
            Pseudo Genes (ambiguous residues) :: 0 of 172
            Pseudo Genes (frameshifted)       :: 74 of 172
            Pseudo Genes (incomplete)         :: 112 of 172
            Pseudo Genes (internal stop)      :: 38 of 172
            Pseudo Genes (multiple problems)  :: 46 of 172
            Pseudo Genes (short protein)      :: 1 of 172
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063710.1.
            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..3272
                     /organism="Salmonella enterica subsp. enterica serovar
                     Enteritidis"
                     /mol_type="genomic DNA"
                     /strain="A1636"
                     /serovar="Enteritidis"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149539"
                     /plasmid="pSE-GC"
                     /geo_loc_name="Malawi"
                     /lat_lon="13.2543 S 34.3015 E"
                     /collection_date="1998"
                     /collected_by="MLW"
     gene            complement(74..232)
                     /locus_tag="IRO96_RS23480"
     CDS             complement(74..232)
                     /locus_tag="IRO96_RS23480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(887..1081)
                     /locus_tag="IRO96_RS23035"
     CDS             complement(887..1081)
                     /locus_tag="IRO96_RS23035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2192..3031)
                     /locus_tag="IRO96_RS23040"
     CDS             complement(2192..3031)
                     /locus_tag="IRO96_RS23040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677176.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_000546749.1"
                     /translation="MHIEEEDLRALERAVELLAQDTITETLTQLVGTPIDYLMSKLPKG
                     AEKKIYSLVEKSLNKAANAALWSLDNEPNRIASTKTNKFFAALSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFDLDRIDTKLECLAVFSYGGPSEDDDAVNTAYYATRNLT
                     AEIVQDLSKEISNITVKNAASTQTGKWLASLIEKVATRFGIVITEKMAAQAAPVIGALA
                     GATLNTMFTDYYQDMARGHFIVKRLERKYGDELIKAEYIKISDKLTNQNQRKHLNSN"
                     /name="EcsC family protein"
     Typing          730..814
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          1118..1216
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          1341..1596
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="89.0"
                     /evalue="1.25e-96"
     Typing          complement(161..710)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.833"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggggactgct taaccgggta actggcttgg tggagcacag ataccaaata ctgtccttct
       61 agtgtagccg cagttaggcc accacttcaa gaactcttaa tatctcaatc caccttgtcc
      121 agttaccagt ggctgctgcc agtggcgctt tgtcgtgtct taccgggttg gactcaagac
      181 gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca
      241 gcttggagcg aacgacctac accgaactga gataccaaca gcgtgagcta tgagaaagcg
      301 ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag
      361 gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt
      421 ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat
      481 ggaaaaacgc cagcggcgcg gcctttcgtt gccctttgcc tttttgctca catgttcttt
      541 ccggccttat cccctgattc tgtggataac cgtattaccg cctttgagtg agccggcacc
      601 gctcgccgca gccgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc
      661 ctgatgcggc attttctcct tacgcatctg tgcggtattt cacatcgcat atggtgctct
      721 tttcttataa tctgtactga tgctacatag ttaagccagt atacactccg ctatcgctac
      781 gtgactggtt cagggcttcg ccccgaaacc ccctgacgcg ccctgacggg cttgtctgct
      841 gacgaaaacg cccacgggaa agccgtgacc gcctccgtca gcttcgttat gttcctgttt
      901 cactttcggc ctcaaagcga atctggatgc tgttctggag ttcttctgcg agttcgtgca
      961 gtcgttcgca catggccgcc tgttcgtcgg catccagagc atccagtttt tcaagcagtg
     1021 tcaggctctg gcttttgata aatcgcgcca tattcagcgc agtttgttgt tgtttgttca
     1081 ccttccgttg ttctccgtca gttccgggtg tcggggggac cctgagcagg tggtaattgt
     1141 aagacgttgc gggcgacggt attacaattg cacatcctgt cctgtttctt taggacgtat
     1201 catggcacag catatcaact gataaataat ccctgtgcag tgcagccgct gttgcataaa
     1261 atttcgctct gcgtcgagtg tttcttaatc aataattccg ctgatactcc ggaaaaacgc
     1321 gagtctgttc tcatgcctga aatgcccaca ccccacgcaa aaacaatttt ttgctgattt
     1381 ttctttataa atagagagtt atgacaaatt agttcttctt gctctctttg tgatatttaa
     1441 aaaagcggtg tcggcgcagc tacaacaccg cgccgacacc gctttttagg ggtggtactg
     1501 actattttca taaaaaacat cattttatat taggggtgct gctagctgcg cggtgtgttt
     1561 ttttacagga cgcccctggg ggcgctgcca ggggtgtctg ttcagatatg tagcaatgag
     1621 tcagggattc acgaactgaa aatgtccgaa aatgtgtctc atgggcactg tatgcgccca
     1681 aaccgatcgt cattcacttt catgcatagc tatgcagtga gctgaaagcg agcctgacgc
     1741 atttttccgg tttaccccgg ggaaaacatc tctttttgcg gtgtttgcgg cagaatcgcg
     1801 ttcagcgcgt tttagcggtg cgcgcaatac gggattatgg taaatatgat tgatattcgt
     1861 agatgctggg ttaactattt attttgtgcg tggagttgaa attggtaatg attagaatgg
     1921 ctatgaccta taaatgttta tcatgccatt ggtgtaaaac tgtgcctaaa tgtagcgatg
     1981 ttttagttga tggggggaat gcttttagtc agtgcccaaa ttgtggctct gttttagttg
     2041 attcaaaaaa agccaatttc attaatgcag ttgttgcgaa tataatgttt aaaataaaat
     2101 cataaataat tttgttgttt gtgtgattgt tcgtgagttg acaccctcca tagcacctgg
     2161 ccataacggt gctatgcact tagtgaaacc gttagttgct gttcaaatgc ttccgttggt
     2221 tctgattggt gagtttatct gagattttta tatattcagc ctttatcaat tcatcaccat
     2281 attttctctc aagtcttttg acaataaaat gacctcgagc catatcttga taatagtcgg
     2341 taaacatcgt gtttaatgtg gctccagcca gtgctccaat aacaggagca gcttgagctg
     2401 ccattttttc tgtaataact ataccaaatc ttgtcgcaac tttttctatt aacgaagcta
     2461 accattttcc tgtttgtgtt gaagcagcgt tcttgacagt aatgttagaa atttctttgg
     2521 ataaatcttg tacgatctca gcagtcaaat tccttgttgc atagtatgca gtattaactg
     2581 catcatcgtc ctcagatggt cctccgtagg aaaacaccgc taaacactct agttttgtat
     2641 caatcctatc tagatcaaaa ccttcacttc ttgctatgtc cgcaattgaa cgaagcataa
     2701 ttgtcgttga aactggtaac tcaattgcta atgcagaaaa gccaaaagca ccaccaatgg
     2761 ctccagataa ggcagcaaag aacttatttg tcttagttga tgctattcgg ttaggttcat
     2821 tgtctaggct ccataaggct gcattagcag ctttgttgag agatttttct actaggctat
     2881 aaattttctt ttctgctcct ttgggaagtt tactcattaa gtaatctatt ggggttccaa
     2941 ctaattgggt tagtgtttct gtaattgtat cttgtgctaa taattctacg gctctttcta
     3001 aagcgcgcag atcttcttct tcaatatgca tgtaaaaatc ccttatgaat caatctgtag
     3061 cctacttttt gtaagtggtc tgttttggga tcttaccttg ggagaattca gtgattcaac
     3121 gggcgagatg ccgatatcat tgttgtccgt gaagtaggag tgatgaaaag atcaaaggat
     3181 cctcttgaga tccttttttt ctgcgcgtaa tctgctgcca gtaaacgaaa aaaccgcctg
     3241 gggaggcggt ttagtcgaag gttaagtcag tt
//
