LOCUS       NZ_CP050774             4677 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI102
            plasmid pSI102-3, complete sequence.
ACCESSION   NZ_CP050774
VERSION     NZ_CP050774.1
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 4677)
  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  JOURNAL   Unpublished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 4677)
  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
            CP050774.1.
            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..4677
                     /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="pSI102-3"
                     /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            1282..2580
                     /locus_tag="HEC79_RS24085"
                     /old_locus_tag="HEC79_24085"
     CDS             1282..2580
                     /locus_tag="HEC79_RS24085"
                     /old_locus_tag="HEC79_24085"
                     /inference="COORDINATES: protein motif:HMM:NF024700.4"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_064987013.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESGITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFISGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            2585..3022
                     /locus_tag="HEC79_RS24090"
                     /old_locus_tag="HEC79_24090"
     CDS             2585..3022
                     /locus_tag="HEC79_RS24090"
                     /old_locus_tag="HEC79_24090"
                     /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_052918195.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     gene            complement(3257..3370)
                     /locus_tag="HEC79_RS24660"
                     /old_locus_tag="HEC79_24095"
     CDS             complement(3257..3370)
                     /locus_tag="HEC79_RS24660"
                     /old_locus_tag="HEC79_24095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072101919.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(4007..4201)
                     /locus_tag="HEC79_RS24100"
                     /old_locus_tag="HEC79_24100"
     CDS             complement(4007..4201)
                     /locus_tag="HEC79_RS24100"
                     /old_locus_tag="HEC79_24100"
                     /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"
     Typing          3850..3934
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          4238..4336
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          4448..4677
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="80.0"
                     /evalue="7.63e-84"
     Typing          complement(3299..3836)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.993"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tttttttaca ggacgcccct gggggcgctg ccaggggtgt ctgttcagat atgtagcaat
       61 gagtcaggga ttcacgaact gaaaatgtcc gaaaatgtgt ctcatgggca ctgtatgcgc
      121 ccaaaccgat cgtcattcac tttcatgcat agctatgcag tgagctgaaa gcgagcctga
      181 cgcatttttc cggtttaccc cggggaaaac atctcttttt gcggtgtttg cggcagaatc
      241 gcgttcagcg cgttttagcg gtgcgcgcaa tcggatgtta tggtaaatcc agctgattgg
      301 caggtataaa aaagccgtcc gtagacggcc tagtaagtta cttcgtcttt gtcatcacta
      361 ccaattccca tcggatgtca cctgggacat tatgctgcct atgattttgc ggtggcaaag
      421 gatcatcttt attgcacgtc acttcatcac cacagttcgt gcagcggtaa atgccggaag
      481 ccggacaagt atttcccggc ttatagtaat accgccatac actcccttca ggctcggttg
      541 tttttgttaa aaatttcgct gtgctatcta cataaaaggc catgttgctt tccttacata
      601 aactaagtta gggaccgaag cttgcatgct tcggtggtta ttgttttttc ttttcccgat
      661 taattgggat cttaaacatt cccccgttag gacgggttat ccgtttgccc tttaccgtta
      721 tgtaagggcg aaaaatgtat gcctgaggct cgtccgtctg catgttgcat ttcctatttt
      781 cgccacatga atgttgattt ttgctatcaa aattgtactg tagcaaccaa cagatcttgt
      841 ggctggcttt atcaaagcac ttgaggtggt actcaagcgc cgcatttgcg tatggtttgt
      901 tacgggttag ttctggtggt acaggctaac ccacttactt caacaatttt tgcttctcct
      961 cattcatgtt tcactctcta cgtatttttt tacagtgtca gcgccactga gcataaacgc
     1021 gacaaaaagg aaccatcccc acccagatac cgagtgaaaa gccagcactg ctgagctaat
     1081 cactgaggca aatgggacca tttggtatag aaaaaacttc atatacacct ctttttaagc
     1141 tggtcgttaa cttatctact cataatgtgc tgtctattgg acccttttgt tgttttagta
     1201 cggggttatg ctattcttaa tctagaattt tgtcaatatt gtgcaatttt tgagtttaag
     1261 ggtgttgtta ggggtgttct tatgatggtt aactttagtc tttcaaacgc attttccttc
     1321 atggaagctc aaaatatgag catgttggcg gtgtcgtcat cgaaagacga tataaacttg
     1381 gctaatgtag tgtcagtaag ggatgagcgg atactgaagt ctgctttgat tttcggagct
     1441 aacgctagcg gaaaatctaa tctcatgaag acaatatctt taatgaaaga tattgtcctg
     1501 cattctgtgc aagctatcga aagtggcatt acgaagaatg tagtcccttt tttacttgat
     1561 gaggcggggc ctactaaacc atctgaaatg gaaatgactt ttattgcgga tgggattaaa
     1621 tacagatacg gattatcttt atttcaaggg aagataaaag aagagtggtt gtactacacg
     1681 ccaaaaacaa gggagactat tctctttgag cgagatggtc aacttattga aataaataaa
     1741 gcagcattta gcgagtcaaa tctttttata aaggatgggg tcattcagaa gacaagagaa
     1801 gatgttccct ttgtttctgt tgttgctgga tttaatgggg agcactcaaa gcgtgttgtg
     1861 aattggttta gtaatgtggt atttatttct ggttctaacg aaggaatgtt tactggaatt
     1921 accatgaagc ttataaatga atctgaagat tttaaagctt ggctaaaaaa aatattacca
     1981 gcctttcaga ttaatgatat ttatcttgat gaagttgcgc ctgaattccc gtttggcaac
     2041 ataaaaacag atgatgataa tttaaaaaat ttattcagct cgattcagaa ttttgcaaaa
     2101 aatcaaaaag tattttctct tagagtcgtg aaaaaaactg ctaatgggga gatttcggtt
     2161 cccattgatt ttgaatcaga ggggaccaaa aagatagtct atctccttgg gcctatttat
     2221 aacgccatga ttaacaataa cttattattg gttgatgagt tcgattcaaa gttccatacc
     2281 cttttatcta agtttttatt taggatattt catgcgcaaa gtgaagggtt tagccaagta
     2341 atcgctgcag ttcaggatgt taatttaatg aatactgatt gctttagacg agaccaaatt
     2401 tggtttgttg acaaggatgt aaagtcaggg agtagccatc tttattcttt ggttgagtac
     2461 aaagagaaac aaagatcatt gaagccatca tatgggaatg attatttatc aggtgctttt
     2521 gatgcaatcc cgttatttga taatcttaat gaatttgaaa agctaatgcc tgagggatga
     2581 ttatatgcca aagagaggca aaagcattcg aagctcttcg aggaatgagg aaacaaaacc
     2641 ttcaaagagc acagcgaaaa cgactgatag atttatatct attagtttta agcattttca
     2701 taacgtcgat gatgttgggc agtccataaa tacatggaaa gatgatggta gcctacctga
     2761 tctcattgaa aaattggttt atctaacggc gaatggaatc actaaagtga tttctgacgg
     2821 tgtgtttact aactacactc gatttcctga gtcagctgta aacgatttta gatgcccaga
     2881 tgagatatcc tctgatgagg attggggggt tataaaaaac attggcgggc agaaaagaag
     2941 agtcgccgga tttctgagag ataatgtgtt ctatatcgtg ttttttgata gagatcatcg
     3001 cttctggaag agtcaaaaat agatgagata cagttgtatt gtatgttaag aaaagatctt
     3061 cttgagattg tgatgctctc gtcgtaatct cttgctctgt aaacgaaaaa accgccttgg
     3121 cgggcggttt ttcgacggtt ctaagagttg gcgctctgtg aaccaaggta actggcttat
     3181 gaggagcgca gtaaccaaat ctgttctttc agtttagcct taacaggcgc ataacttcaa
     3241 gactaactcc tctaaatcag ttaccagtgg ctgctgccat tggcgttttg tcgtgtcttt
     3301 ccgggttgga ctcaagttga tagttaccgg aaaaggcgca gcggtcggac tgaacggggg
     3361 gttcgtgcat acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg
     3421 gaatgagaca aacgcggcca taacagcgga gtgacaccgg taaaccgaat ggcaggaaca
     3481 ggagagcgca cgagggagtc accaggggga aacgcctggt atctttaagt cctgtcgggt
     3541 ttcgccacct ctgacttgag cgtcggtttt tgtgatgctc gtcagggggg cggagcctat
     3601 ggaaaaacgc cagcggcgcg gccttcctcc tgttcctggt cttttgctca catgttcttt
     3661 ccggccttat cccctgattc tgtggataac tgtgttaccg tttttgtgtg agtcagtacc
     3721 gctcgccgca gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaaaagcgc
     3781 ctggacatgc attttctcct tacgcatctg tgcggcattt cacacccggc atggcgtact
     3841 tttcatacaa tccgcactga tgccgcatgg ttaagccagt atacactccg ctatcgctac
     3901 gtgactggtt cagggcttcg ccccgaaacc ccctgacgcg ccctgacggg cttgtctgct
     3961 gacgaaaacg cccacgggaa agccgtgacc gcctccgtca gcttcgttat gttcctgttt
     4021 cactttcggc ctcaaagcga atctggatgc tgttctggag ttcttctgcg agttcgtgca
     4081 gtcgttcgca catggccgcc tgttcgtcgg catccagagc atccagtttt tcaagcagtg
     4141 tcaggctctg gcttttgata aatcgcgcca tattcagcgc agtttgttgt tgtttgttca
     4201 ccttccgttg ttctccgtca gttccgggtg tcggggggac cctgagcagg tggtaattgt
     4261 aagacgttgc gggcgacggt attacaattg cacatcctgt cctgtttctt taggacgtat
     4321 catggcacag catatcaact gataaataat ccctgtgcag tgcagccgct gttgcataaa
     4381 atttcgctct gcgtcgagtg tttcttaatc aataattccg ctgatactcc ggaaaaacgc
     4441 gagtctgttc tcatgcccga aatgcccaca ccccacgcaa aaacaatttt ttgctgattt
     4501 ttctttataa atagagagtt atgacaaatt agttcttctt gctctctttg tgatatttaa
     4561 aaaagcggtg ttggcgcagc tacaacaccg cgccgacacc gctttttagg ggtggtactg
     4621 actattttca taaaaaacat catcttatat taggggtgct gctagctgcg cggtgtg
//
