LOCUS       NZ_CP050781             4234 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI85
            plasmid pSI85-2, complete sequence.
ACCESSION   NZ_CP050781
VERSION     NZ_CP050781.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450152
            Assembly: GCF_012054045.1
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  JOURNAL   Unpublished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                     :: SI85
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 76x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012054045.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 02:49:03
            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)                     :: 4,871
            CDSs (total)                      :: 4,751
            Genes (coding)                    :: 4,584
            CDSs (with protein)               :: 4,584
            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)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 63 of 167
            Pseudo Genes (incomplete)         :: 127 of 167
            Pseudo Genes (internal stop)      :: 33 of 167
            Pseudo Genes (multiple problems)  :: 47 of 167
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050781.1.
            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="SI85"
                     /serovar="Indiana"
                     /isolation_source="Chicken product"
                     /host="chicken"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pSI85-2"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2012-08-24"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            join(2743..4234,1..728)
                     /gene="mobQ"
                     /locus_tag="HEC77_RS24150"
                     /old_locus_tag="HEC77_24150"
     CDS             join(2743..4234,1..728)
                     /gene="mobQ"
                     /locus_tag="HEC77_RS24150"
                     /old_locus_tag="HEC77_24150"
                     /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_151577630.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLIHDYTRK
                     RGVDDAVILTPANAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLLRTYRAVKERDIPVRRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITELG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPV
                     LALPSPDYSHLMVSIITENGIHLAGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHFRGMSM"
                     /name="mobQ"
     gene            1175..2083
                     /locus_tag="HEC77_RS24155"
                     /old_locus_tag="HEC77_24155"
     CDS             1175..2083
                     /locus_tag="HEC77_RS24155"
                     /old_locus_tag="HEC77_24155"
                     /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(2289..2564)
                     /locus_tag="HEC77_RS24160"
                     /old_locus_tag="HEC77_24160"
     CDS             complement(2289..2564)
                     /locus_tag="HEC77_RS24160"
                     /old_locus_tag="HEC77_24160"
                     /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"
     Typing          complement(2569..2742)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="98.0"
                     /evalue="1.23e-74"
     Typing          complement(2743..3101)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1176..1903
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.376"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          4..725
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.627"
                     /coverage="99.0"
                     /evalue="1.14e-141"
     Typing          2744..4233
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.97"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cggtgaatgt ttacctgtcg ccaggcgggg ctgtgatggt ctcggatata cgtgagggaa
       61 tgccagaatc tcatgagacg atggcgcggc ctgagcgtgt gagaatgtat tccggtgcga
      121 cggtccggca tgtactggaa cagatgcgcc aggggtggcc ctcttacggt tttccggcgc
      181 tgccgcatca ctggccggat aatttttatt tcagcgacga ccgcaggccc gcagcctctc
      241 cgctgccgtc agcgcaccgg gtggacgtca ccgcttatgc ggcaccggag caactcatgc
      301 ccgttgtctt ttcgacagag cgaaacagca ggacgctgaa tctgctgttg tgcaaagggc
      361 cggaggaaat gcttgtcggt tttgtgcgcc tggaggacga gctgcgtccc gttcttgcgc
      421 ttccgtcgcc ggattacagt catctgatgg taagcatcat cacagagaac gggatacacc
      481 tggcaggcta cggtgaggcc ataaaccgtg atgctgatac tccgtaccca ccggaaccga
      541 agctgatgca gttcaggctt aagggctgtc aggacacgct ttttgctgcc atcaacaaac
      601 cggaagagat gccggattat ctcttccgtc aactcggatt taatcagacc tggcatgaat
      661 ggaagcggga cgaacagcac aggcaacaac aacgacgtcc cgggcacttc cggggcatga
      721 gtatgtgata tccggggctg caccccgaac cccgccaacg tctcacggga cacgaaaaaa
      781 ttccgcgtcc cgtgaggcgt tttctggatg agaaagtttg ccgttttgac ccgttcgcgc
      841 ttctgaacgg tcgaaaccga tcgcgcatcg ctttcgtgaa tagttatgca gacccctgaa
      901 aacgattctg acgcgttttt ctggtttggc ctggtgtttt cttgtctttt tgtgtttttt
      961 gcgtcagaac gcgtctgaga gcgttttaag gggtacgtac aacaggagtt atggtaaatg
     1021 gatcggtttt tcgggaagga tcgacaggat ttgccgttgg gtgtagtgta agcgactgaa
     1081 aaacaaacgc ccctgaaatt cgtgtagatc cgccaagact ttcacgaaga tacaggggcg
     1141 atgtcggtcg ataacctgga aggaatcgta acacatgagc gccgcgcttc aatacttcga
     1201 agaaaattta cctcaccgtc cctatcacac ggatgatccc gctttcggcc ttcgcatctc
     1261 cggcaaaggg cgtgcgcttc ttgcgcggta cattcagcag aaccagccac atgcgcaaca
     1321 ctggctggtt tttgacgttg accgcgaggg ggctgcgatt gactggagcg accggaacgc
     1381 ccccgcgccg aacatcaccg taaaaaatcc cgtgaatggg cacgctcacc tgctatacgc
     1441 gctcaatctt gccgtgagaa ccgcgcctga tgcgtcggtt aaggtgctga aatacgccgc
     1501 tgcaattgaa cgtgcgctgt gtgagaaact tgacgcagat gtgaactaca gcggactgat
     1561 ttgcaaaaat ccgttccacc tggaatggca ggtgatggag tggcgcgagg aagcctatac
     1621 cctcgatgaa ctggctgatt atctcgattt gagcgcctca gagcgtcgta gcgtcgataa
     1681 acattacggg ctggggcgaa actgccacct gttcgaaata acgcgtaaat gggcttacag
     1741 agcgattcgt cagggatggc cagcattctc acagtggctt gatgccgtga tccagcgtgt
     1801 cgaaatgtac aacgcatcgc ttcccgttcc tctttcactg gctgaatgcc gggctattgg
     1861 caagagcatt gcgaaataca cgcacagaaa attctcaccg gaaggctttt ccgctgtaca
     1921 ggccgctcga ggccggaaag gtggccttgc taaaggcgaa gcctacgagg acaagcgttt
     1981 catggcgcta tgtatgctgg agaatggata ttctcagaaa gctattgcgg cgatgctgga
     2041 tgtacatcga aatacgatcc gtaattgggc aatgcacaaa tagccttatc agataacagc
     2101 gccttttcgg cgcttttttg agctgttggc gttcctgcgg tttttccggt tccgcccagc
     2161 aatggcgctg gtttcctcgt gattgcggtg gtagcgctcg ccgcagcctc atgaccgagc
     2221 gtagcgagcg aatgtgcgag gaagcgcaaa ggcgtccggt ggtgcatgtg gcacttacgc
     2281 gccggggctt atccgttctg cggtttcgca ggtggtcttg gtagcttctc cagctcgtta
     2341 atcagtggtt gtagccggtt cacatcggcc tgtcttgtga cttcctttcg caggaactgg
     2401 agcaggaacg cacgcagttg cgcctcttcc ggcctccgta ccctcgccag catggctgct
     2461 cccacaatga ctttttgcgc agtgtccagg ctccggctct tcgccttcag gcgctgcaat
     2521 ctggcctcag cttcagcaat cttctgttcg agtgttctgc tcatttcgtg actccttgcg
     2581 cggtgaaaaa tcgcatttta gctcgtcact ggtagtttaa aaactgagct ggcataatgc
     2641 acggcatatc acgaagtgcg cacttataca atcttcactt cgtttcgatt gtgtgcgccc
     2701 tgcggggctg aaagaaaacg gcaaaaaggc attacggcag aaatggcgat ttatcatctc
     2761 agcatgaaaa tcatttcgcg aaaaaacggc tacagtgccg ttgcttctgc tgcctaccgt
     2821 tccggctctg tcatacccga tgaccgtacc ggattaatcc acgattacac ccgtaaacgc
     2881 ggcgttgatg atgcggtcat tctcacccct gcgaatgcac cgtcctggtg tggtgaccgt
     2941 tccgttctct ggaatgcggt cgagaaagcc gaacagcgcc ggaactccca gctggcaagg
     3001 gagattgaac tcgccattcc ccgtgagatt tcccgcgagg ccgcacggga ggccgttctc
     3061 gcttttgtcc gggaaaactt tgtcagtcgg ggcatgattg ccgatgtggc gttccatcat
     3121 atggaccgga ccaaccccca tgcacacatc atgctgacca cgagagctgt cggggaaacg
     3181 ggattcgcag gaaaggtcag ggactggaac gaccgggcac tcgccgagac gtggcgcgca
     3241 tcatgggctg accatgcgaa cagagcgctt gcgaacgccg gctaccagga agagatagac
     3301 catcgttcat acgagcgtca gggactggag aaagcgccgg gccttcacct cggaaaggct
     3361 gcctgtgcga tggaaaaacg gggcatggaa acagaacgcg gtgagcagaa ccgcctgatt
     3421 aacagcctta acctggaaat acaggtttcc cgcacaaggc tggcagtcat ccaggtacag
     3481 gagaacgtgc ggaaacggga actcagcgat gccgcacgtc gtgcagcgga agcccttaat
     3541 ctgaccattc ccgccgcgaa tgcctcagcg gataccctgc gggaattcat tgccacactg
     3601 ccgcaggaat gcgggaacgc atgggagatg acaccggagt tcgtggcgat gaacgggaag
     3661 gcaaacgaca tcaaacgtga ggggaatgcg ctggtgaaag agcgggatat tctcgaaaaa
     3721 gagatgaccg gactcagaaa agcccgtccg gtagcgtcca tcctgtcaga gcttcccctg
     3781 atgacatggg ctgaaccgga ataccgcaaa agacaactcc gcttctggaa actcgagaaa
     3841 cagattgaat ctcttctccg cacctacagg gccgtgaaag aacgggacat tcccgtccgt
     3901 cgtcaggcct ttgaaacgca gtggaatacg tggatttcgc cgggaatggc agagctgaaa
     3961 gaaaaactgt cagcacggga agcggagcgg cgcagggagg aagccgaagc ggaagcgcgc
     4021 cggaaggaac aggaatatga cgcacggctg aaacaccatg ataaccatcg cctgagccga
     4081 gaaacggcat tagccggggt tattacggag ctggggcgtg ccagagagcc gggaacgggc
     4141 aggataaccc gctacatgat gctgagtaac agagccggag aattcacggt atggggtgat
     4201 gagctggcgc attaccccca gagtgttcat gacc
//
