LOCUS       NZ_CP050776             2677 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI102
            plasmid pSI102-5, complete sequence.
ACCESSION   NZ_CP050776
VERSION     NZ_CP050776.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450154
            Assembly: GCF_012052605.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Indiana
  ORGANISM  Salmonella enterica subsp. enterica serovar Indiana
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2677)
  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  JOURNAL   Unpublished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 2677)
  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                     :: SI102
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 202x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012052605.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 02:38:15
            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)                     :: 4,865
            CDSs (total)                      :: 4,745
            Genes (coding)                    :: 4,581
            CDSs (with protein)               :: 4,581
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 164
            CDSs (without protein)            :: 164
            Pseudo Genes (ambiguous residues) :: 0 of 164
            Pseudo Genes (frameshifted)       :: 67 of 164
            Pseudo Genes (incomplete)         :: 118 of 164
            Pseudo Genes (internal stop)      :: 34 of 164
            Pseudo Genes (multiple problems)  :: 46 of 164
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050776.1.
            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..2677
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="SI102"
                     /serovar="Indiana"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pSI102-5"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2013-01-31"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            join(2545..2677,1..272)
                     /locus_tag="HEC79_RS24120"
                     /old_locus_tag="HEC79_24120"
     CDS             join(2545..2677,1..272)
                     /locus_tag="HEC79_RS24120"
                     /old_locus_tag="HEC79_24120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000014067.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000014067.1"
                     /translation="MSGGNNFKMSQDYEIAQPKKKMAYPILVEEWDFLIGKIESISDDE
                     NIYHTIGSIFLGVAGSALIAALTLDLPSDDGYMPRQILISWYVFWASLICGVLSMFFGR
                     KNKKINRTSAKDIVQQMRLIEKRYEQGSMD"
                     /name="hypothetical protein"
     gene            complement(485..646)
                     /locus_tag="HEC79_RS24665"
                     /old_locus_tag="HEC79_24125"
     CDS             complement(485..646)
                     /locus_tag="HEC79_RS24665"
                     /old_locus_tag="HEC79_24125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_071527578.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDLSPLAAATGNRIRGVSLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(1116..1310)
                     /locus_tag="HEC79_RS24130"
                     /old_locus_tag="HEC79_24130"
     CDS             complement(1116..1310)
                     /locus_tag="HEC79_RS24130"
                     /old_locus_tag="HEC79_24130"
                     /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_001041622.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1594..1917
                     /gene="mobA"
                     /locus_tag="HEC79_RS24135"
                     /old_locus_tag="HEC79_24135"
     CDS             1594..1917
                     /gene="mobA"
                     /locus_tag="HEC79_RS24135"
                     /old_locus_tag="HEC79_24135"
                     /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            2276..2548
                     /locus_tag="HEC79_RS24140"
                     /old_locus_tag="HEC79_24140"
     CDS             2276..2548
                     /locus_tag="HEC79_RS24140"
                     /old_locus_tag="HEC79_24140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001286144.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001286144.1"
                     /translation="MSDVKSDQIIKYLSEKWGGSKCPLCKKGRWNVSDKIFELREFHEG
                     NVVIGAGPIVPIIPVTCDNCGNVVLVNAIISGCLSADNKQDGGSK"
                     /name="hypothetical protein"
     Typing          1349..1585
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          complement(575..1082)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.415"
                     /coverage="95.0"
                     /evalue="2.2999999999999997e-156"
     Typing          1595..1914
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.47e-63"
ORIGIN
        1 aaaatatata ccatacgatt ggttctatat ttttaggtgt ggctggctcg gcattgatag
       61 cagcattaac tttagatttg ccatcagatg atggttatat gccaaggcag atattaattt
      121 catggtacgt attttgggca agccttattt gtggagtgct ttctatgttt tttggtagaa
      181 agaataaaaa gattaataga acttctgcga aggatattgt gcaacaaatg agattgatag
      241 agaaacgtta cgagcaaggt agtatggatt aactggatgc tgaacgttta gcgaggttac
      301 ggcgtgccaa ggggggggca taatgtaagg atcttcttga gatccttgtc ttgtcgtcgt
      361 agtctcttgt ctatgaaacg aaaaaaccac ccggcaaggt ggtttttcga aggttctcag
      421 agctaccaac tctttgagcc gaggtaactg gcttggagga gcgcagtcac caaaacttgt
      481 tctttcagtt tagccttaac aggcgcatga cttcaaggct aactcctcta attcggttac
      541 cagtggctgc tgccagtggc gataagtcgt gtctttccgg gttggattca agtcgatagt
      601 taccggataa ggcgcagcgg tcggactgaa cggggggttc gtgcatacag tccagcttgg
      661 agcgaactgc ctacccggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac
      721 tgcggaatga cattggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagcttcca
      781 gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccacctctg acttgagcgt
      841 cggtttttat gatgctcgtc aggggggcgg agcctatgga aaaacgcctc ccgcgcgccc
      901 ttcttctggg tctttgtctt ttgctcacat gttctttccg gttttatccc ccgattctgt
      961 ggataaccgt attaccgcct ttgagtgagc tgacaccgct cgccgcagtc gaacgaccga
     1021 gcgtagcgag tcagtgagcg aggaagcgga agagcgcctt atgtgacatt ttctccttac
     1081 gctcctctat gccgttctgc atcctgtctg gagcgttata tcccggtaag attttccgct
     1141 tcaaagcgtg tctgtatgct gttctggagt tcttctgcga gttcgtgcag tttctcacac
     1201 atggcggcct gttcgtcggc attgagtgcg tccagttttt cgagcagcgt caggctctga
     1261 ctttttatga atcccgccat gttgagtacg gcttgctgct gcttgttcat cttttcgttt
     1321 tctccgttct gtctgtcatc tgcgttgtgt gattatatcg cgtaccactt ttcgactgtt
     1381 ttgctgccgc tattctgccg cttggctttt tgacgggcat ttctgtcaga caacactgtc
     1441 actgccaaaa aactgccgtg cctttgtcgg taattcgagc ttgctgacag gacaggatgt
     1501 gcaattgtta taccgcgcat acatgcacgc tattacaatt gccctggtca gggctttgcc
     1561 ccgacaccca tgtcagatac ggagccatgt tttatgacaa aacgaagtgg aagtaatacg
     1621 cgcaggcggg ctatcagtcg ccctgttcgt ctgacggcag aagaagacca ggaaatcaga
     1681 aaaagggctg ctgaatgcgg caagaccgtt tccggttttt tacgggcggc agctctcggt
     1741 aagaaagtta actcactgac tgatgatcgg gtactgaaag aagttatgag actgggggcg
     1801 ttacagaaaa aactctttat cgacggcaag cgtgtcgggg acagggagta tgcggaggtg
     1861 ctgatcgcta ttacggagta tcaccgtgcc ctgttatcca gacttatggc agattagctt
     1921 cccggagaga aaactgtcga aaacagacgg tatgaacacc gtaagctccc aaagtgatca
     1981 ccattcgctt tcatgcatag ctatgcagcg agctgaaaac gatcctgacg catccttcct
     2041 gttttcccgg ggtaaaacat ctctttttgc ggtgtctgcg tcagaatcgc gttcagcgcg
     2101 tttcagcggt gcgtacaata ctggtattat ggtaaatgta agattttata tttatgtttt
     2161 tttgcgcaca aaacagatat ggatgtactc tataaagtta cttgatcaat aaattattga
     2221 gtgatgtgat tgttcgctaa taaatatatg agtataagga atgcttggag ggaatatgag
     2281 tgatgttaag tcagatcaaa taattaaata tttgtctgaa aagtggggag ggagcaaatg
     2341 tcccttgtgt aaaaaagggc gttggaatgt ttctgacaaa atttttgaac taagagaatt
     2401 tcatgaaggt aatgttgtta ttggggcagg tccgatagtc ccaattattc ctgtaacttg
     2461 tgataattgc gggaatgttg ttcttgttaa tgccattatc tcagggtgct tatctgctga
     2521 caataagcaa gatggaggct caaagtgagt ggtggtaata attttaaaat gtctcaggac
     2581 tatgaaattg ctcaaccaaa aaagaaaatg gcttacccta ttcttgttga agaatgggat
     2641 tttttaatag ggaaaataga aagtattagt gatgatg
//
