LOCUS       NZ_CP092261             5632 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain 15
            plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP092261
VERSION     NZ_CP092261.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25873476
            Assembly: GCF_022350005.1
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 5632)
  AUTHORS   Chao,G. and Wang,X.
  TITLE     The Large Plasmid Carried Class 1 Integrons Mediated Multidrug
            Resistance of Foodborne Salmonella Indiana
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5632)
  AUTHORS   Chao,G. and Wang,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-FEB-2022) College of Veterinary Medicine, Yangzhou
            University, 88 South University Ave., Yangzhou 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 31-DEC-2019
            Assembly Method                   :: ABySS v. v2.0.2; CANU v. v1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 423.0x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022350005.1-RS_2024_05_08
            Annotation Date                   :: 05/08/2024 06:41:45
            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)                     :: 4,884
            CDSs (total)                      :: 4,765
            Genes (coding)                    :: 4,603
            CDSs (with protein)               :: 4,603
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 63 of 162
            Pseudo Genes (incomplete)         :: 120 of 162
            Pseudo Genes (internal stop)      :: 33 of 162
            Pseudo Genes (multiple problems)  :: 46 of 162
            Pseudo Genes (short protein)      :: 1 of 162
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092261.1.
            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..5632
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="15"
                     /serovar="Indiana"
                     /host="broiler chickens"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="unnamed3"
                     /geo_loc_name="China:Changzhou"
                     /collection_date="2017-06-08"
     gene            1..327
                     /locus_tag="MF259_RS24325"
                     /old_locus_tag="MF259_24325"
     CDS             1..327
                     /locus_tag="MF259_RS24325"
                     /old_locus_tag="MF259_24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_042927524.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRR
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDTLTPSERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            536..>958
                     /locus_tag="MF259_RS24330"
                     /old_locus_tag="MF259_24330"
                     /pseudo=""
     CDS             536..>958
                     /locus_tag="MF259_RS24330"
                     /old_locus_tag="MF259_24330"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1005..1490
                     /locus_tag="MF259_RS24335"
                     /old_locus_tag="MF259_24335"
     CDS             1005..1490
                     /locus_tag="MF259_RS24335"
                     /old_locus_tag="MF259_24335"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_072035998.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMIRTSVSAAMAWVFLCFALLIGIMGGIIWFQGTIITSRLSEMD
                     SYSQQLANLKAKSGAGVAIYSDDKHRNTYMVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            1560..1784
                     /locus_tag="MF259_RS24340"
                     /old_locus_tag="MF259_24340"
     CDS             1560..1784
                     /locus_tag="MF259_RS24340"
                     /old_locus_tag="MF259_24340"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_226939304.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1946..2278
                     /locus_tag="MF259_RS24345"
                     /old_locus_tag="MF259_24345"
     CDS             1946..2278
                     /locus_tag="MF259_RS24345"
                     /old_locus_tag="MF259_24345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000017531.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKIRMATGNQGKSGSVRVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2280..2564
                     /gene="nadS"
                     /locus_tag="MF259_RS24350"
                     /old_locus_tag="MF259_24350"
     CDS             2280..2564
                     /gene="nadS"
                     /locus_tag="MF259_RS24350"
                     /old_locus_tag="MF259_24350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            2757..3659
                     /locus_tag="MF259_RS24355"
                     /old_locus_tag="MF259_24355"
     CDS             2757..3659
                     /locus_tag="MF259_RS24355"
                     /old_locus_tag="MF259_24355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652796.1"
                     /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_239450411.1"
                     /translation="MNNAVLELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     SDKDIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYDQWLQACYERASAYNLQFPAPLD
                     EKEVNGIAKSIAKWTEKNFTASSFKEYVINSHRSDIQSKRGRLGGLKSKGGGRPTINSP
                     WESMGISKSTYYRNIHGKR"
                     /name="replication initiation protein"
     gene            3646..5406
                     /locus_tag="MF259_RS24360"
                     /old_locus_tag="MF259_24360"
     CDS             3646..5406
                     /locus_tag="MF259_RS24360"
                     /old_locus_tag="MF259_24360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AIPR family protein"
                     /protein_id="WP_057515538.1"
                     /translation="MARDDFNSDTRTVGLARLANSLEETYGSFINMENTNSKGEARREV
                     LITRCIAAHAVRMYGDELDPGVAAASVCDGSDDGGIDAVYVNPSSKKLILVQSKYIKDG
                     NGSVTIKDFGRFKDACAKVIANDLNSFNDRFLEHKESVTTAITSSSYKCICVFIYSGTQ
                     GLSSEVIGEIDFWEKSQNKALLFRDLESRDEYTILFETPNVTDISTSLSNQSTGAIDIS
                     NVILESYGEITEPYGAIYGTIAARVIHDWWKKYKYALFEKNIRSVLGDSTSVNAGIMST
                     IENSPENFWYYNNGITATYEEVDESIANAGASRKIGIFGFKKLNIINGAQTVSSIGAIF
                     DSIPEEKKDKARVMIRFINAKDPVFLGDVTKYNNTQNRVTGRDFTTQRPEQQKIQREIN
                     FVGGYTYKLLRQEDSGIAASNVIDIDDSLNALICESKKPQLIATLKSNRGRFFDTTEGN
                     LYEQVFNPRNPPSGISVINAVNLYRVCFDVLKDTITKASNSSEDEYSKIPSLLTHGNYV
                     FISILMGKIQPINTVNGIKTYDKNSVSFDTLELAKSIFEYIQSNYPNSYLARFFQNKEK
                     VEQIITHFSS"
                     /name="AIPR family protein"
     Typing          318..1882
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.743"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggaaaagc gaacgaaaga gatcaaaatc cggctcaccg aaaccgagca tcagcgactg
       61 cttgatcgct gcgaccggac tcaccttgcg gagtggctgc gtcagcttgg tctgggtgaa
      121 cacacttcac gcaggcgccg tgtgcccgat gtggcgcccg aattgctgcg acaggtcagc
      181 ggaatcggta acaacctgaa ccagattgcc cgccgtctga accagactga caccctgacg
      241 ccctctgaac gtgcttcgct gcttgtcgta ctgactagcc ttgatcggca gcttggcgac
      301 ctgctggagc agaaccgtga tcgttaaaat tcattcgcgg ggtgcgggtt cgggcagcgg
      361 tcctgtggat tacctgctgg gaaaagaccg gcagcgcgaa caggctagcg tactgcgcgg
      421 caatcctgaa catgtgcgtg agctgatcga cggctgcaac tttgcccgcg cctacacttc
      481 cggcgtgctt tcattccagg aacctgacat tgcagacgcc gagaaatcgc gcctgatgga
      541 cgaatgggag cacacgctgc tgaccggact cgaccgcgac cagtacgcct gcctgtgggt
      601 agagcatcgc gacaagggac ggcttgagct gaattttgtc atcccgaaca tcgaattgca
      661 gagtggaaaa cgcctgcaac cctactttga ccgcgccgac cgtccccgcg tcaacgcctg
      721 gcagaccctg accaacgacc ggctggggct gcgcgacccg aatgacccga cctaccgccg
      781 tccgctgacg caggccagcg atctgccccg cgacaaacag caggcggcag agaaaatcac
      841 cgccggcctg atgaacctga tgcagcaggg cgtgatccgc agccggcagg acgtggtgac
      901 gcagctggaa agctacggcc tgaccgtagc gcgggaaacg aaaagtagca tcagcattgc
      961 cgatccggac ggcggccgaa atatccggct gaaaggaatg atttatgagc gagattttaa
     1021 atttggcgaa gggcttcgag gagaaatcga agcagcaggc gcaggatacc gagcagagcg
     1081 tgaagcgcga gttcgcgagg ctggagacgt ctatcagcgc ggaactgcaa tcaagctcgc
     1141 agagcatcag caacgctatc cgcgagcaga acggcaggct gacgggcatg atcagaacct
     1201 ccgtttcagc ggcgatggcg tgggtattcc tctgcttcgc cctgctgatc ggcatcatgg
     1261 gggggataat ctggtttcag ggtacgatca tcacctcgcg cctgagcgaa atggacagct
     1321 acagccagca gctggcgaac ctgaaagcga aaagcggcgc gggcgtggcg atctacagcg
     1381 acgacaagca ccggaacacc tacatggtgg tgctgccgaa gcaggcgcac ggcgtggaaa
     1441 cctatacatc gacgaccgac aacaccgtag tgaaatacac ggcgaaataa ccccgtcaga
     1501 gcgccctgaa acgacacagc gcgtttttaa caccgaggat gaccaaaacc atgaccgaga
     1561 tggaaaaaca gcttctgagc gccttagaga gcttacagac aagctacgag caacagcagc
     1621 aggcgtggca ggacagctac agcagcttgc agcacatgtt cgaggctacc tcacaggcgc
     1681 tgacgcacag cgaccgggtg tgtcagcact tgagcagtca ggtagagagc ttgcgcgcgc
     1741 aggtcgagag cttgagcagg aacgtcagcc gcttgatgcg ttgatcaggc agcacgaccg
     1801 cgcctacgcc gagaagctgc gtgagcagca gccagagccg gagccgcaga aaaaaacgac
     1861 ccgctactat ggcccctcga tgtgaccgct tttccgaaat cagaattaag tgtactatgt
     1921 actccgttaa aaacaggaga cagccgtgag tcacgcgatt gagtttatcg agaccccgat
     1981 gtttacccgt cagataaaac agatcgccac ggatgaagaa ctcagggagc tgcaaaagac
     2041 gctgattgag tcgccggaca aaggcgatct cattcagaaa accggcgggc tgcgcaaaat
     2101 caggatggcg acgggcaacc agggaaaaag cggcagcgtg agggtgattt actttctggc
     2161 caccgccgag gtgatctatc tggtgatggc ctacccgaaa agcaccaaag acagcctgac
     2221 ggacgcggaa aaagccgcgc tgaagacgct gacccaacaa ctgaaagacg aggtgtgaca
     2281 tgagtttttt tgacgagctg aaagcatcgc tggaagaagc cgttgaaatc aaaaacggcg
     2341 tcagagagcc tgcccgcgtc acccgttacg agctggcaga cgtgaaagcc atcagggcac
     2401 agctgaacgt atctcagagc gagatggcga aagtgctggg aaccagcctc gacaccatca
     2461 agagctggga aaccggacgc cgtaacccga ccggactggc ggcgaaggta ctggcaacca
     2521 tccaggcgaa cccgaaattc ttccaggaac tggcggcgca ctaagccgtt gtgacagaag
     2581 gattagacag gcgaggccgt tcgcgtgtaa tttaacggca acagaaaaaa caaagccccg
     2641 gaaatcatgc tcaatcttgg cggatgcaca tgataaccag ggccaggtcg aaaccttgaa
     2701 aggatattag cacatgaaac gtgccagaca acagcccgcc ataagcgcag ggcgaattga
     2761 ataacgcagt actcgaactt ttcaacgacc gcttaccgca caagccgtac ttctcggatg
     2821 atttacactt tggtgtacgc attgcaggga aagaacgcgc cattctggcg aaatacatcc
     2881 agttcaatca gcctcacgcc atgttctggc tgggattcga cgtcgatcgc gccggtgccg
     2941 ccatcgactg gagcgatcgc aacgcgcccg cgcccacgct gaccatcacc aacccggaaa
     3001 acggacacgc gcacctgctg tacgcgctgg aaacctcgat acgcaccgca cctgacggga
     3061 aaatgaagcc gctgcgctac gccgctgccg tggagaatgc gctacgtaaa aaattagagg
     3121 ctgatgcggg gtattcggga ctaatctgca aaaatccgaa ccacggacac tggaaaattg
     3181 ccgtatggca gccggaactc tacacgctgg actggctggc tgattttctc gacctgaatg
     3241 cagcgagcga caaagacatc gttgctgact acggcttagg ccgtaactgc accctgttcg
     3301 acaaaacccg caaatgggca taccgcgcca tccgtcaggg ctggccggag tatgaccagt
     3361 ggctacaagc ctgctacgaa cgcgcaagtg cttacaatct gcaattccct gcacctctgg
     3421 atgaaaaaga ggtgaatggg atagctaaaa gcattgcaaa atggactgaa aaaaacttta
     3481 cagcatcttc atttaaagag tacgtaatta actctcatag aagcgatatt caatctaaaa
     3541 gaggtcgttt aggcggatta aaaagcaaag gtggcggcag gccaacaata aactccccgt
     3601 gggaaagtat ggggattagt aaatcgacat attacaggaa tattcatggc aagagatgat
     3661 tttaatagcg acactagaac cgttgggctt gcaaggttag ctaatagcct agaagaaacc
     3721 tatggttctt ttattaatat ggaaaacact aactctaaag gtgaggctag aagagaagtt
     3781 ctgatcacaa gatgcattgc tgcgcatgca gtaaggatgt atggtgatga actcgaccct
     3841 ggagttgctg ctgcatcagt ttgcgatggt agcgatgatg ggggaattga tgctgtttat
     3901 gtaaacccaa gttctaaaaa acttattttg gtacagtcaa aatatataaa agatgggaat
     3961 ggttctgtaa caataaaaga ttttggacgg tttaaagacg catgtgcaaa agttatagct
     4021 aacgatctca attcatttaa tgatagattt ttagagcaca aagaatcagt gactacggct
     4081 atcactagta gtagctataa atgcatatgc gtttttattt attcaggaac ccaagggtta
     4141 agctcagaag tgattggaga gattgatttt tgggagaaaa gccaaaacaa agcgctgttg
     4201 tttagagatt tagaatctag ggatgagtat acaatactat ttgaaacgcc taatgttact
     4261 gacatatcta ctagcttgag caatcaatct accggagcta tagatataag taatgtaata
     4321 ttagagtcgt atggtgagat cactgaacct tacggcgcaa tctacggaac gattgctgca
     4381 agggtgatac atgattggtg gaaaaaatac aagtatgcgc ttttcgagaa aaatataaga
     4441 agtgtcttgg gtgattcgac atcagtaaat gcagggatca tgtctaccat cgaaaatagc
     4501 ccagagaact tttggtacta taacaacggg attactgcaa catatgaaga ggtagatgag
     4561 agcatagcta atgctggagc atctcggaaa attggaatat tcggatttaa aaagttaaac
     4621 ataataaatg gggcgcaaac tgtaagctct attggggcta tatttgatag catacccgag
     4681 gagaaaaaag acaaagctcg agtgatgatt aggtttataa atgcgaaaga tcctgttttt
     4741 ttaggtgacg taactaagta caacaatact cagaatagag ttactggcag agatttcaca
     4801 acacaaagac ctgaacagca aaaaatacag agagaaataa actttgttgg gggttataca
     4861 tataagctct tacgacagga agattcaggg atagctgctt ctaatgttat cgatatagat
     4921 gactcattaa atgcactaat ttgcgaatca aagaaacctc aacttattgc aactttgaag
     4981 tctaatagag gtcgtttttt tgatacaaca gagggcaatc tttacgaaca agtttttaac
     5041 ccaagaaatc cgccatccgg tatttctgtt atcaatgctg ttaatttata cagagtatgt
     5101 ttcgatgttt taaaagatac aattactaaa gcatctaact catcagaaga tgaatatagt
     5161 aaaattccat cactgctgac gcatggtaac tatgtattta ttagtatttt aatggggaaa
     5221 atacaaccca taaatacagt taatggcata aaaacctatg acaagaatag cgtctctttt
     5281 gatactcttg aactagctaa aagcatattt gaatacatcc agtctaatta tcctaacagc
     5341 tatctggcta gatttttcca gaacaaagaa aaagtagagc agatcatcac tcacttttca
     5401 tcgtgagact aaacaagcct atatcagata acagccctct ctagcagagg gctttttttt
     5461 gcagccacca cataatctga tatactgcac cttacactaa gccagtacac acagcgtccc
     5521 ctctaacgag gtgccactgt gactggttca gggggctcgc cgccccccga aacccccggc
     5581 atccactgcg aaaaattctc acagtggtgc gaattttctc tcagcggagc ct
//
