LOCUS       NZ_CP050720             3005 bp    DNA     circular CON 22-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Enteritidis strain SE95
            plasmid pSE95-4, complete sequence.
ACCESSION   NZ_CP050720
VERSION     NZ_CP050720.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450171
            Assembly: GCF_012050385.1
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 3005)
  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  JOURNAL   Unpublished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 3005)
  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                     :: SE95
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 34x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012050385.1-RS_2024_03_22
            Annotation Date                   :: 03/22/2024 03:52:47
            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)                     :: 4,762
            CDSs (total)                      :: 4,642
            Genes (coding)                    :: 4,446
            CDSs (with protein)               :: 4,446
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 196
            CDSs (without protein)            :: 196
            Pseudo Genes (ambiguous residues) :: 0 of 196
            Pseudo Genes (frameshifted)       :: 81 of 196
            Pseudo Genes (incomplete)         :: 130 of 196
            Pseudo Genes (internal stop)      :: 40 of 196
            Pseudo Genes (multiple problems)  :: 49 of 196
            Pseudo Genes (short protein)      :: 1 of 196
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050720.1.
            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..3005
                     /organism="Salmonella enterica subsp. enterica serovar
                     Enteritidis"
                     /mol_type="genomic DNA"
                     /strain="SE95"
                     /serovar="Enteritidis"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149539"
                     /plasmid="pSE95-4"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2013-06-19"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            join(2943..3005,1..99)
                     /locus_tag="HEC96_RS24220"
     CDS             join(2943..3005,1..99)
                     /locus_tag="HEC96_RS24220"
                     /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_309248314.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHAKAPLAAAIGNRVSRARFV
                     QMLTEFLK"
                     /name="replication initiation protein"
     gene            300..977
                     /locus_tag="HEC96_RS23635"
                     /old_locus_tag="HEC96_23635"
     CDS             300..977
                     /locus_tag="HEC96_RS23635"
                     /old_locus_tag="HEC96_23635"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023233475.1"
                     /translation="MENKAVTISTQLAIFIDSTIARPDLLFNSLNSEIGEVIDAMPQTL
                     PLPADAPADIPRVIGTSSFGKFNLNISLNRIDFVENYTPTEEIEKSVTEFKLKCNTLIA
                     TIFQKYGVVRIGLVGNYYIPHKNPSQLIADLYLNENKRNLDEITIRINNRDTFKNIQIN
                     NVINLSQGQVTAQNYNGNAVIVQLDYNSTDNNTPLDEGLTLALFKEKSIAYNSKHVEDV
                     SGL"
                     /name="hypothetical protein"
     gene            974..1357
                     /locus_tag="HEC96_RS23640"
                     /old_locus_tag="HEC96_23640"
     CDS             974..1357
                     /locus_tag="HEC96_RS23640"
                     /old_locus_tag="HEC96_23640"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_022631129.1"
                     /translation="MKFFKPKTDAIEYIRVEPSFSKTSSNINNAKSGSDTNSQPGFILR
                     SQIEEMIKNHRPKTEKEIKAESEGLIRLCSMAFIFLIVLSIFMLIVYFGIKDRELPDFA
                     NNLMALMTTLVGAIGGFIYGTKK"
                     /name="hypothetical protein"
     gene            complement(1666..1989)
                     /gene="mobA"
                     /locus_tag="HEC96_RS23645"
                     /old_locus_tag="HEC96_23645"
     CDS             complement(1666..1989)
                     /gene="mobA"
                     /locus_tag="HEC96_RS23645"
                     /old_locus_tag="HEC96_23645"
                     /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_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2262..2456
                     /locus_tag="HEC96_RS23650"
                     /old_locus_tag="HEC96_23650"
     CDS             2262..2456
                     /locus_tag="HEC96_RS23650"
                     /old_locus_tag="HEC96_23650"
                     /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_001041644.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1999..2225)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.25"
                     /coverage="99.0"
                     /evalue="2.24e-83"
     Typing          2486..3005
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.066"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(1670..1989)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.96e-62"
ORIGIN
        1 aacccggtaa gacatgcaaa agcaccactg gcagcagcca ttggtaaccg agttagcaga
       61 gcgagatttg tccagatgct tacagagttc ttgaagtgat ggcctgacta cggctacact
      121 agaaggacag tatttggtat ctgcgctctg ctgaagccag ttacccggtt agacaatctg
      181 ccaggattag ctaaccttcg aaaaaccacc tgccagggtg gttttttcgt ttaagatact
      241 cacaacacgt taatttcgca atacttcaat taataccaat gcaaaatagg aaagaaaaaa
      301 tggaaaacaa ggccgtcaca atatcaacac agctagcaat atttattgac agcaccatag
      361 ctagaccaga tcttctcttt aatagcctaa actcagaaat tggcgaagtt atagacgcaa
      421 tgccacagac gcttcccctg cctgcagatg cacctgcaga tatccctcgc gttattggca
      481 catcgtcctt tggcaagttc aacttaaaca tatcactaaa cagaatagat tttgtagaaa
      541 actacacccc tactgaggag atcgaaaaat cagtaacgga attcaaatta aagtgcaata
      601 cgctaatagc aacaatattc caaaaatatg gagtcgtaag aatcggccta gttggtaact
      661 attacatccc acataaaaat ccatctcaac taatagctga tctgtattta aacgaaaaca
      721 aaagaaattt agatgaaata acaataagaa taaataaccg cgatacattc aaaaatatac
      781 aaataaacaa tgtcatcaat ttaagccaag gacaagtaac cgcacagaac tacaatggaa
      841 atgcggtgat agttcaactt gactacaact caaccgataa taacacacca cttgacgaag
      901 ggttaacctt agccctattt aaagaaaaat ccattgctta taactccaag catgttgagg
      961 atgtgagtgg attatgaaat ttttcaaacc aaaaacagat gcgattgaat acattcgtgt
     1021 agaaccatca ttctcaaaaa caagtagcaa tataaataat gcgaaatcag gaagtgacac
     1081 aaactcacag cctggattca ttttaagatc tcaaatagag gaaatgataa aaaaccacag
     1141 accgaaaaca gaaaaagaaa taaaggctga aagcgaaggt cttataaggc tttgctccat
     1201 ggcctttata tttttaatag ttttatcaat ttttatgtta atcgtttatt tcggaataaa
     1261 agatagagaa ctaccagatt ttgcaaataa cctgatggca ctaatgacaa cattagttgg
     1321 agcgataggt ggttttatat atggaacaaa aaaataacac agacaaaaac acaaataaaa
     1381 aaaacaaata acacacaagc acaccagccc catacttcgg ggcttttaca accgttacct
     1441 gacaccattt accataacat ctcattacgc gcaccgccaa aacgcgctga acgcgattct
     1501 gacgcagaca ccgcaaaaag agatgttttc cccggggtaa accggaaaaa tgcgtcagga
     1561 ttgctttcag ctcactgcat agctatgcat gaaagtgaat ggcgatcggt ttgggggctt
     1621 acggtgttca taccgtctgt tttcgacagt tttctccccg ggaagctaat ctgccataag
     1681 cctggataac agggcacggt gatactccgt aatagcgatc agcacctccg catattccct
     1741 atccccgaca cgcttgccgt cgataaagag ttttttctgt aacgccccca gtctcataac
     1801 ttctttcagt acccgatcat cagtcagtga gttaactttc ttaccgagag ctgccgcccg
     1861 taaaaaaccg gaaacggtct tgccgcattc agcagccctt tttctgattt cctggtcttc
     1921 ttctgccgtc agacgaacag ggcgactgat agcccgcctg cgcgtattac ttccacttcg
     1981 ttttgtcata aaacatggct ccgtatctga catggggtgt cggggcaaag ccctgaccag
     2041 ggtaattgta atagcgtgca tgtatgcgcg gtataacaat tacacatcct gtcctgtcag
     2101 caagctcgaa ttaccgacaa aggcacggca gttttttggc agtgacagtg ttgtctgact
     2161 gaaatgtccg tcggcagaat accggcggta agacggtcca aaagtggtgc gcgatataat
     2221 cacacgacgc agatgacaga cagaacggag aaaacagaaa gatgaacaag cagcagcaaa
     2281 ctgtactcaa catggcggga ttcataaaaa gccagagcct gacgctgctc gaaaaactgg
     2341 acgcactcga tgctgacgag caggccacca tgtgtgagaa gctgcacgaa ctcgcagaag
     2401 aactccagaa cagcatacag acacgctttg aagtagaaaa tagcacagag atataacgct
     2461 cagggcagga tgccgaacgg cacaacagag cgtaaggaga aaatgtcaca taaggcgctc
     2521 ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt cgactgcggc gagcggtgtc
     2581 agcgcactca aaggcggtaa tacggttatc cacagaatca ggggataaag ccggaaagaa
     2641 catgtgagca aaaagcaaag caccggaaga agccagcacc gcaggcgttt ttccataggc
     2701 tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga
     2761 caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc
     2821 cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt
     2881 ctcatagctc acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct
     2941 gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg
     3001 agtcc
//
