LOCUS       NZ_CP050715             3374 bp    DNA     circular CON 22-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Enteritidis strain SE104
            plasmid pSE104-3, complete sequence.
ACCESSION   NZ_CP050715
VERSION     NZ_CP050715.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450172
            Assembly: GCF_012050525.1
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 3374)
  AUTHORS   Chen,Z.
  TITLE     Genomic analyses of multidrug-resistant Salmonella Indiana,
            Typhimurium, and Enteritidis isolates using MinION and MiSeq
            sequencing technologies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3374)
  AUTHORS   Chen,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-2020) Joint Institute for Food Safety and Applied
            Nutrition, University of Maryland, 5145 Campus Drive, Patapsco
            Building, Suite 2134, College Park, MD 20742, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: SE104
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 113x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012050525.1-RS_2024_03_22
            Annotation Date                   :: 03/22/2024 03:53:40
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,770
            CDSs (total)                      :: 4,649
            Genes (coding)                    :: 4,456
            CDSs (with protein)               :: 4,456
            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)              :: 193
            CDSs (without protein)            :: 193
            Pseudo Genes (ambiguous residues) :: 0 of 193
            Pseudo Genes (frameshifted)       :: 76 of 193
            Pseudo Genes (incomplete)         :: 132 of 193
            Pseudo Genes (internal stop)      :: 40 of 193
            Pseudo Genes (multiple problems)  :: 49 of 193
            Pseudo Genes (short protein)      :: 1 of 193
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050715.1.
            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..3374
                     /organism="Salmonella enterica subsp. enterica serovar
                     Enteritidis"
                     /mol_type="genomic DNA"
                     /strain="SE104"
                     /serovar="Enteritidis"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149539"
                     /plasmid="pSE104-3"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2013-07-10"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            join(3320..3374,1..137)
                     /locus_tag="HEC97_RS23705"
                     /old_locus_tag="HEC97_23705"
     CDS             join(3320..3374,1..137)
                     /locus_tag="HEC97_RS23705"
                     /old_locus_tag="HEC97_23705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1455..1688)
                     /locus_tag="HEC97_RS23710"
                     /old_locus_tag="HEC97_23710"
     CDS             complement(1455..1688)
                     /locus_tag="HEC97_RS23710"
                     /old_locus_tag="HEC97_23710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1695..2255)
                     /locus_tag="HEC97_RS23715"
                     /old_locus_tag="HEC97_23715"
     CDS             complement(1695..2255)
                     /locus_tag="HEC97_RS23715"
                     /old_locus_tag="HEC97_23715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_167797738.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISGHTTSVKQQLDTLSATVSTQFSTTEAELSRQQKKLLWQVIKGRILFPALTA
                     LSVTGGIFLGGWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2287..2943)
                     /locus_tag="HEC97_RS24120"
                     /old_locus_tag="HEC97_23720"
                     /pseudo=""
     CDS             complement(<2287..2943)
                     /locus_tag="HEC97_RS24120"
                     /old_locus_tag="HEC97_23720"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            complement(2933..3256)
                     /locus_tag="HEC97_RS23725"
                     /old_locus_tag="HEC97_23725"
     CDS             complement(2933..3256)
                     /locus_tag="HEC97_RS23725"
                     /old_locus_tag="HEC97_23725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(219..299)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(1373..2943)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgctaaccct gctggaaaaa ctcaacgatc tggacgcgga cgaacaggca gacatctgcg
       61 aatcacttca cgaccacgcc gacgaactct accgcagttg cctcgcacgc ttcggcgatg
      121 acggtgaaag caactgaaac atgcagctcc cggagacgtt cacagcttgc ctgtgagcgg
      181 atgccgggag cagacaagcc cgccagggcg cgtcagtgcg ggtgtcgggg cgcagccctg
      241 acccagttca cagagcgata gcgatgtgta tactggctta tctcattttg catcggtgca
      301 gacatggatg ggaagtgcac catgtcagga gtaaaaagcc gcacagatgt aaaaacagcg
      361 cacccgataa acagcacaca cgcggacact ggcacaggcg cgtaagtgca caatgcttgc
      421 atctgtgact cttccgcttc ctcgcccact cgctcactac gttcggtcgc tggggctgcg
      481 gcgagcggtg ggatcactct cgttgtgatg cagatccgtt tttttttttt tgcactggag
      541 ttatcaggag ttgcggtgca catgggatcg tgcgatatgc cggatggtga aaggttggag
      601 ggaacggcaa caactcaccc ctcccagtga agggacgggt agtttgccgc tctcgatatg
      661 ccggacggag ccaaggccat cgatcacggg gcgcgtcagt ggaagaaccc gcgcctgcgt
      721 gacgtatgcg tcttcgccgc accatctcac ccgtcacgcc accacatacc gggaactgcc
      781 gccaaggtct aactcaacca atctagccgc gctacatacg gtttttgtgg caactcatca
      841 ggtgtccgct gtcgatgaaa ctctctgcgc cggtagcgga actctcacgc gtgcggtcgc
      901 cgtcgtcaca gctcccccaa ccgcaaacga ttctcgcaaa tacgcaagta tctgcaaaaa
      961 caggtttttt tcggggttcc tgggagactg tgctgttgaa aaattcttga agaatacaga
     1021 aggctcatgc aaactgaatg aactggtttc tgttgtggat ctcaacagtt tccacaggaa
     1081 cattgaggag gtcagagacc tcaatgaacc cgaaacagct cgccttcctg gcgagctgtt
     1141 ttcgttctac gcccgccgac gaaagatcgc aagtgcaata acgagatttt tcacgtcttt
     1201 acgctcaaaa agtaaaaaaa ccatgttttc ccctggctga atccccaaaa acgcgtgaaa
     1261 tgcgttttca ggatgttgca tagctatgca caaatacggc acacgatttg tttcgctcgc
     1321 cccagccgtc gaactggtca aaatggcaag atttcgtcac ttccccggtc acatctccat
     1381 tgatggccca ctccgaaccc gtgccgcgcg ttcctgtacc tcatgtctgt accgggcacg
     1441 ctcctgttca tcccttagct gttgttcgcg ataaataacc gactcaagcg atccacttgc
     1501 ccggctaatc tctgcacctg ctgactcaat atcacgacgc gctcgttcag tatcgcgttg
     1561 ttccgttgcg taacctcgtg catcttctgc aattccgcga aggcgctctc ccactcgttc
     1621 agccgccgca tatagtcctg ttgcaaatgc tctaaggcgt tcagcaaatg cccttccagt
     1681 tccgtcatac tcgtttactc cctgaccagc ctcacggcgt tcttgtcgcc caccgtccag
     1741 gtgttttccc ctttcacccc gtccggcaac accagaaatt tcccgttctc gccattgacg
     1801 aacgtcaccc cccaggtttt tgcctcgagt ttcgccagcg tgttttcctg ctctctgata
     1861 gtcaggatat ttttcgcaat cttgctttcc tgccactcca tcagccccca gccccccagg
     1921 aaaatgccgc ccgtgacgct gagcgcggtc agcgccggaa acagtatccg ccctttgatc
     1981 acctgccaga gcagtttttt ctgctgccgg gacagttcgg cctctgtggt gctgaactgc
     2041 gtgctcacgg tggcgctcag tgtatccagt tgctgtttca cggatgttgt atgtccgctg
     2101 atagcgtctc tgattttctg cctgtttaag ctcagtgcct tgtctacaga ctcttcgagc
     2161 ttcctgaact cgctgttcag catgttctcg gtagaagcgg ctcgctcttt cagtttcttc
     2221 tcgaagtctg ttcccatttg taaaagattg ctcatacagc gcccccttta gcctgagatt
     2281 ccgcccaccc tccgggtcgg caatactgat actgcttctg gttgtcctca ccacctcaaa
     2341 acctgccgct gtgagcgcct cagtgacatc ctgacgcgtt tttattgctc cggcatggta
     2401 aagcgcctca agaccccgtg taatcgcttc tgcggcctcc tgtttcgctt ttggcagatt
     2461 atttggcgtg acaagcgtcc gtctgttctc cggtgcgttc gggtcacgca gcccgtaatg
     2521 atgattaacc agcgtctgcc aggcatttat cctcggcctg tccgcgcggt cgtagtacgg
     2581 ctggaggcgc ttaccgctct gtagctccat gttcgggatg acaaaattca gttcgagccg
     2641 ccccttatcc tggtgttcca cccagagaat gctgtactgg tctttttcga gaccgggcat
     2701 aagaacacgc tcaaagctcg tcatcactct ttcgcgttca cccggcggta actccttctc
     2761 cgcgaacgac agaacgcctg aagtgtattt cttcgagaat ggcgtggaat caatgagttc
     2821 ccgcacttct tccgggttac cccggagcac cgttgcgcct tcgcggttac gctcccgccc
     2881 cagcaggtaa tcgaccgggc cacttccacc gcctttcccc ctggcatgaa atttaactat
     2941 catcccgtac cccctgttcc ctgacagcct gccgcaactg gcgcaattca ccctcgatgg
     3001 ccatcagtgc ggccaccaca tgaacccggt caatcgaaga ccactggccg ctgttcacct
     3061 tccgggctgt ctggttcagg ttgttcccga tggcagccag atgccgcagc aatggcggcg
     3121 atagtgtcgg cagttttcct gtgcgtgcaa ccggctcccc cagacagacc cgccgcatcc
     3181 attccgccag tcgtttaccc tcgcagcgtt ccagtaaccg ggcgtgctcc tcatcggtaa
     3241 cccgtatcgt gagcatcttc tcgcgtttca tcggtatcat tccccctaac aaatccccca
     3301 tacaaggagc cttaagacca tgaccaaaca ggaaaaaaca gcccttaaca tggctcgctt
     3361 tatcagaagc caga
//
