LOCUS       NZ_CP050775             4234 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI102
            plasmid pSI102-4, complete sequence.
ACCESSION   NZ_CP050775
VERSION     NZ_CP050775.1
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 4234)
  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  JOURNAL   Unpublished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 4234)
  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
            CP050775.1.
            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..4234
                     /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="pSI102-4"
                     /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(3418..4234,1..92)
                     /locus_tag="HEC79_RS24105"
                     /old_locus_tag="HEC79_24105"
     CDS             join(3418..4234,1..92)
                     /locus_tag="HEC79_RS24105"
                     /old_locus_tag="HEC79_24105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_058657849.1"
                     /translation="MSAALQYFEENLPHRPYHTDDPAFGLRISGKGRALLARYIQQNQP
                     HAQHWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNLAVRTAPDASVKV
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSVDKHYGLGRNCHLFEITRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGLAKGEAYEDKRFMALCMLENGYSQ
                     KAIAAMLDVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(298..573)
                     /locus_tag="HEC79_RS24110"
                     /old_locus_tag="HEC79_24110"
     CDS             complement(298..573)
                     /locus_tag="HEC79_RS24110"
                     /old_locus_tag="HEC79_24110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052995416.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNG"
                     /name="hypothetical protein"
     gene            752..2971
                     /gene="mobQ"
                     /locus_tag="HEC79_RS24115"
                     /old_locus_tag="HEC79_24115"
     CDS             752..2971
                     /gene="mobQ"
                     /locus_tag="HEC79_RS24115"
                     /old_locus_tag="HEC79_24115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_167810811.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLIHDYTRK
                     RGVDDAVILTPANAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLLRTYRAVKERDIPARRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITGLG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPVA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEVLVGFVRQEDGLRPV
                     LALPSPDYSHLIVSTITENGVCLAGYGEAINHDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     Typing          complement(578..751)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="98.0"
                     /evalue="1.23e-74"
     Typing          complement(752..1110)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3419..4146
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.376"
                     /coverage="88.0"
                     /evalue="0.0"
     Typing          753..2968
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.911"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtatgctgga gaatggatat tctcagaaag ctattgcggc gatgctggat gtacatcgaa
       61 atacgatccg taattgggca atgcacaaat agccttatca gataacagcg ccttttcggc
      121 gcttttttga gctgttggcg ttcctgcggt ttttccggtt ccgcccagca atggcgctgg
      181 tttcctcgtg attgcggtgg tagcgctcgc cgcagcctca tgaccgagcg tagcgagcga
      241 atgtgcgagg aagcgcaaag gcgtccggtg gtgcatgtgg cacttacgcg ccggggctta
      301 tccgttctgc ggtttcgcag gtggtcttgg tagcttctcc agctcgttaa tcagtggttg
      361 tagccggttc acatcggcct gtcttgtgac ttcctttcgc aggaactgga gcaggaacgc
      421 acgcagttgc gcctcttccg gcctccgtac cctcgccagc atggctgctc ccacaatgac
      481 tttttgcgca gtgtccaggc tccggctctt cgccttcagg cgctgcaatc tggcctcagc
      541 ttcagcaatc ttctgttcga gtgttctgct catttcgtga ctccttgcgc ggtgaaaaat
      601 cgcattttag ctcgtcactg gtagtttaaa aactgagctg gcataatgca cggcatatca
      661 cgaagtgcgc acttatacaa tcttcacttc gtttcgattg tgtgcgccct gcggggctga
      721 aagaaaacgg caaaaaggca ttacggcaga aatggcgatt tatcatctca gcatgaaaat
      781 catttcgcga aaaaacggct acagtgccgt tgcttctgct gcctaccgtt ccggctctgt
      841 catacccgat gaccgtaccg gattaatcca cgattacacc cgtaaacgcg gcgttgatga
      901 tgcggtcatt ctcacccctg cgaatgcacc gtcctggtgt ggtgaccgtt ccgttctctg
      961 gaatgcggtc gagaaagccg aacagcgccg gaactcccag ctggcaaggg agattgaact
     1021 cgccattccc cgtgagattt cccgcgaggc cgcacgggag gccgttctcg cttttgtccg
     1081 ggaaaacttt gtcagtcggg gcatgattgc cgatgtggcg ttccatcata tggaccggac
     1141 caacccccat gcacacatca tgctgaccac gagagctgtc ggggaaacgg gattcgcagg
     1201 aaaggtcagg gactggaacg accgggcact cgccgagacg tggcgcgcat catgggctga
     1261 ccatgcgaac agagcgcttg cgaacgccgg ctaccaggaa gagatagacc atcgttcata
     1321 cgagcgtcag ggactggaga aagcgccggg ccttcacctc ggaaaggctg cctgtgcgat
     1381 ggaaaaacgg ggcatggaaa cagaacgcgg tgagcagaac cgcctgatta acagccttaa
     1441 cctggaaata caggtttccc gcacaaggct ggcagtcatc caggtacagg agaacgtgcg
     1501 gaaacgggaa ctcagcgatg ccgcacgtcg tgcagcggaa gcccttaatc tgaccattcc
     1561 cgccgcgaat gcctcagcgg ataccctgcg ggaattcatt gccacactgc cgcaggaatg
     1621 cgggaacgca tgggagatga caccggagtt cgtggcgatg aacgggaagg caaacgacat
     1681 caaacgtgag gggaatgcgc tggtgaaaga gcgggatatt ctcgaaaaag agatgaccgg
     1741 actcagaaaa gcccgtccgg tagcgtccat cctgtcagag cttcccctga tgacatgggc
     1801 tgaaccggaa taccgcaaaa gacaactccg cttctggaaa ctcgagaaac agattgaatc
     1861 tcttctccgc acctacaggg ccgtgaaaga acgggacatt cccgcccgtc gtcaggcctt
     1921 tgaaacgcag tggaatacgt ggatttcgcc gggaatggca gagctgaaag aaaaactgtc
     1981 agcacgggaa gcggagcggc gcagggagga agccgaagcg gaagcgcgcc ggaaggaaca
     2041 ggaatatgac gcacggctga aacaccatga taaccatcgc ctgagccgtg aaacggcatt
     2101 agccggggtt attacggggc tggggcgtgc cagagagccg ggaacgggca ggataacccg
     2161 ctacatgatg ctgagtaaca gagccggaga attcacggta tggggtgatg agctggcgca
     2221 ttacccccag agtgttcatg acccggtgaa tgtttacctg tcgccaggcg gggctgtgat
     2281 ggtctcggat atacgtgagg gaatgccaga atctcatgag acgatggcgc ggcctgagcg
     2341 tgtgagaatg tattccggtg cgacggtccg gcatgtactg gaacagatgc gccaggggtg
     2401 gccctcttac ggttttccgg cgctgccgca tcactggccg gataattttt atttcagcga
     2461 cgaccgcagg cccgtagcct ctccgctgcc gtctgcgcac cgggtggacg tcaccgctta
     2521 tgcggcaccg gagcaactca tgcccgttgt attttcgaca gagcgaaaca gcaggacgct
     2581 gaatctgctg ttgtgcaaag ggccggagga agtgcttgtc ggatttgtgc gtcaggagga
     2641 cgggctgcgt cccgttcttg cgcttccgtc gccggattac agtcatctga tagtcagcac
     2701 catcacggag aacggggtat gcctggcagg ttacggagaa gctataaacc atgatgcgga
     2761 tactccgtac ccaccggaac cgaagctgat gcagttcagg cttaagggct gtcaggacac
     2821 gctttttgct gccatcaaca aaccggaaga gatgccggat tatctcttcc gtcaactcgg
     2881 atttaatcag acctggcatg aatggaagcg ggacgaacag cacaggcaac aacaacgacg
     2941 ccccggacat taccggggca tgagtatgtg atatccgggg ctgcaccccg aaccccgcca
     3001 acgtctcacg ggacacgaaa aaattccgcg tcccgtgagg cgttttctgg atgagaaagt
     3061 ttgccgtttt gacccgttcg cgcttctgaa cggtcgaaac cgatcgcgca tcgctttcgt
     3121 gaatagttat gcagacccct gaaaacgatt ctgacgcgtt tttctggttt ggcctggtgt
     3181 tttcttgtct ttttgtgttt tttgcgtcag aacgcgtctg agagcgtttt aaggggtacg
     3241 tacaacagga gttatggtaa atggatcggt ttttcgggaa ggatcgacag gatttgccgt
     3301 tgggtgtagt gtaagcgact gaaaaacaaa cgcccctgaa attcgtgtag atccgccaag
     3361 actttcacga agatacaggg gcgatgtcgg tcgataacct ggaaggaatc gtaacacatg
     3421 agcgccgcgc ttcaatactt cgaagaaaat ttacctcacc gtccctatca cacggatgat
     3481 cccgctttcg gccttcgcat ctccggcaaa gggcgtgcgc ttcttgcgcg gtacattcag
     3541 cagaaccagc cacatgcgca acactggctg gtttttgacg ttgaccgcga gggggctgcg
     3601 attgactgga gcgaccggaa cgcccccgcg ccgaacatca ccgtaaaaaa tcccgtgaat
     3661 gggcacgctc acctgctata cgcgctcaat cttgccgtga gaaccgcgcc tgatgcgtcg
     3721 gttaaggtgc tgaaatacgc cgctgcaatt gaacgtgcgc tgtgtgagaa acttgacgca
     3781 gatgtgaact acagcggact gatttgcaaa aatccgttcc acctggaatg gcaggtgatg
     3841 gagtggcgcg aggaagccta taccctcgat gaactggctg attatctcga tttgagcgcc
     3901 tcagagcgtc gtagcgtcga taaacattac gggctggggc gaaactgcca cctgttcgaa
     3961 ataacgcgta aatgggctta cagagcgatt cgtcagggat ggccagcatt ctcacagtgg
     4021 cttgatgccg tgatccagcg tgtcgaaatg tacaacgcat cgcttcccgt tcctctttca
     4081 ctggctgaat gccgggctat tggcaagagc attgcgaaat acacgcacag aaaattctca
     4141 ccggaaggct tttccgctgt acaggccgct cgaggccgga aaggtggcct tgctaaaggc
     4201 gaagcctacg aggacaagcg tttcatggcg ctat
//
