LOCUS       NZ_CP089314             3374 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain YZ21MCS4
            plasmid pYUYZMCS4, complete sequence.
ACCESSION   NZ_CP089314
VERSION     NZ_CP089314.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23799606
            Assembly: GCF_021228955.1
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 3374)
  AUTHORS   Wang,J.
  TITLE     whole genome of Salmonella enterica serovar Indiana YZ21MCS4
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3374)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-DEC-2021) Key Laboratory of Prevention and Control of
            Biological Hazard Factors (Animal Origin) for Agrifood Safety and
            Quality, Ministry of Agriculture of China, Yangzhou University,
            No.48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio RS
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/17/2024 07:47:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,598
            CDSs (total)                      :: 4,480
            Genes (coding)                    :: 4,333
            CDSs (with protein)               :: 4,333
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 60 of 147
            Pseudo Genes (incomplete)         :: 105 of 147
            Pseudo Genes (internal stop)      :: 32 of 147
            Pseudo Genes (multiple problems)  :: 43 of 147
            Pseudo Genes (short protein)      :: 1 of 147
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP089314.1.
            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..3374
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="YZ21MCS4"
                     /serovar="Indiana"
                     /isolation_source="retail chicken meat"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pYUYZMCS4"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.15 N 119.01 E"
                     /collection_date="2021-03"
                     /collected_by="Jiang Yue"
     gene            join(2858..3374,1..44)
                     /locus_tag="LT987_RS22965"
                     /old_locus_tag="LT987_22965"
     CDS             join(2858..3374,1..44)
                     /locus_tag="LT987_RS22965"
                     /old_locus_tag="LT987_22965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            51..284
                     /locus_tag="LT987_RS22970"
                     /old_locus_tag="LT987_22970"
     CDS             51..284
                     /locus_tag="LT987_RS22970"
                     /old_locus_tag="LT987_22970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1602..1793)
                     /locus_tag="LT987_RS22975"
                     /old_locus_tag="LT987_22975"
     CDS             complement(1602..1793)
                     /locus_tag="LT987_RS22975"
                     /old_locus_tag="LT987_22975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1857..2180
                     /locus_tag="LT987_RS22980"
                     /old_locus_tag="LT987_22980"
     CDS             1857..2180
                     /locus_tag="LT987_RS22980"
                     /old_locus_tag="LT987_22980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2389..>2826
                     /locus_tag="LT987_RS22985"
                     /old_locus_tag="LT987_22985"
                     /pseudo=""
     CDS             2389..>2826
                     /locus_tag="LT987_RS22985"
                     /old_locus_tag="LT987_22985"
                     /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"
     Typing          1438..1521
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="95.0"
                     /evalue="4.11e-16"
     Typing          2171..3372
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.259"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 ggacggtggg cgacaagaac gccgtgaggc tggtcaggga gtaaacgagt atgacggaac
       61 tggaagggca tttgctgaac gccttagagc atttgcaaca ggactatatg cggcggctga
      121 acgagtggga gagcgccttc gcggaattgc agaagatgca cgaggttacg caacggaaca
      181 acgcgatact gaacgagcgc gtcgtgatat tgagtcagca ggtgcagaga ttagccgggc
      241 aagtggatcg cttgagtcgg ttatttatcg cgaacaacag ctaagggatg aacaggagcg
      301 tgcccggtac agacatgagg tacaggaacg cgcggcacgg gttcggagtg ggccatcaat
      361 ggagatgtga ccggagaagt gacgaaatct tgccattttg acccgttcga cggctggggc
      421 gagcgaaaca aatcgtgtgc cgtatttgtg catagctatg caacatcctg aaaacgcatt
      481 tcacgcgttt ttggggattc agccagggga aaacatggtt tttttacttt ttgagcgtaa
      541 agacgtgaaa aatctcgtta ttgcacttgc gatctttcgt cggtgggcgt agaacgaaaa
      601 cagctcgcca ggaaggcgag ctgtttcggg ttcattgagg tctctgacct cctcaatgtt
      661 cctgtggaaa ctgttgagat ccacaacaga aaccagttca ttcagtttgc atgagccttc
      721 tgtattcttc aagagttttt caacagcaca gtctcccagg aaccccgaaa aaaacctgtt
      781 tttgcagata cttgcgtatt tgcgagaatc gtttgcggtt gggggagctg tgacgacggc
      841 gaccgcacgc gtgagagttc cgctaccggc gcagagagtt tcatcgacag cggacacctg
      901 atgagttgcc acaaaaaccg tatgtagcgc ggctagattg gttgagttag accttggcgg
      961 cagttcccgg tatgtggtgg cgtgacgggt gagatggtgc ggcgaagacg catacgtcac
     1021 gcaggcgcgg gttcttccac tgacgcgccc cgtgatcgat ggccttggct ccgtccggca
     1081 tatcgagagc ggcaaactac ccgtcccttc actgggaggg gtgagttgtt gccgttccct
     1141 ccgaccttcc accatccagc atatcgcacg atcccatgtg caccgctact cctgataact
     1201 ccagtgcaaa aaaaaaaaac ggatctgcat cacaacgaga gtgatcccac cgctcgccgc
     1261 agccccagcg accgaacgta gtgagcgagt gggcgaggaa gcggaagagt cacagaggca
     1321 agcattgtgc acttacgcgc ctgtgccagt gtccgcgtgt gtgttgttta tcgggcgcgc
     1381 tgtttttacg catctgtgcg gctttttact cctgacatgg tgcacttccc atccactctg
     1441 caccgatgca aaatgaggaa agccagtata cacatcgcta tcgctctgtg aactgggtca
     1501 gggctgcgcc ccgacacccg cactgacgcg ccctggcggg cttgtctgct cccggcatcc
     1561 gctcacaggc aagctgtgaa cgtctccggg agctgcatgt ttcagttgct ttcaccgtca
     1621 tcgccgaagc gtgcgaggca actgcggtag agttcgtcgg cgtggtcgtg aagtgattcg
     1681 cagatgtctg cctgttcgtc cgcgtccaga tcgttgagtt tttccagcag ggttagcgtc
     1741 tggtttctga taaagcgagc catgttaagg gctgtttttt cctgtttggt catggtctta
     1801 aggctccttg tatgggggat ttgttagggg gaatgatacc gatgaaacgc gagaagatgc
     1861 tcacgatacg ggttaccgat gaggagcacg cccggttact ggaacgctgc gagggtaaac
     1921 gactggcgga atggatgcgg cgggtctgtc tgggggagcc ggttgcacgc acaggaaaac
     1981 tgccgacact ggcaccgcca ttgctgcggc atctggctgc catcgggaac aacctgaacc
     2041 agacagcccg gaaggtgaac agcggccagt ggtcttcgat tgaccgggtt catgtggtgg
     2101 ccgcactgat ggccatcgag ggtgaattgc gccagttgcg gcaggctgtc agggaacagg
     2161 gggtacggga tgatagttaa atttcatgcc agggggaaag gcggtggaag tggcccggtc
     2221 gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa cggtgctccg gggtaacccg
     2281 gaagaagtgc gggaactcat tgattccacg ccattttcga agaaatacac gtcaggcgtt
     2341 ctgtcgttcg cggagaagga gctaccaccg ggtgaacgcg aaagagtgat gacgagcttt
     2401 gagcgtgttc ttatgcccgg tctcgaaaaa gaccagtaca gcattctctg ggtggaacac
     2461 caggataagg ggcggctcga actgaatttt gtcatcccga acatggagct acagagcggt
     2521 aagcgcctcc agccgtacta cgaccgtgcg gacaggccga ggataaatgc ctggcagacg
     2581 ctggttaatc atcattacgg gctgcgtgac ccgaacgcac cggagaacag acggacgctt
     2641 gtcacgccaa ataatctgcc aaaagcgaaa caggaggccg cagaagcgat tacacggggt
     2701 cttgaggctc tttaccatgc cggagcaata aaaacgcgtc aggatgtcac agaggcgctt
     2761 acagcggcag gttttgaggt ggtgaggaca accaaaagca gcatcagtat tgccgacccg
     2821 gagggggggc ggaatctcag gctaaagggg gcgctgtatg agcaatcttt tacaaatggg
     2881 aacagacttc gagaagaaac tgaaagagcg agccgcttct accgagaaca tgctgaacag
     2941 cgagttcagg aagctcgaag agtctgtaga caaggcattg agcttaaaca ggcagaaaat
     3001 cagagacgct atcagcgaac atacaacatc cgtgaaaaag caactggata cgctgagcac
     3061 caccgtgagc atgcagttca gcaccacaga ggccgaactg tcccggcagc agaaaaaact
     3121 gctctggcgg gtgatcaaag ggcggatact gtttccggcg ctgaccgcgc tcagcgtcac
     3181 gggcgggatt ttcctggggt gctgggggct gatggagtgg caggaaagca agattgcgaa
     3241 aaatatcctg actatcagag agcaggaaaa cacgctggcg aaactcgagg caaaaacctg
     3301 gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg gtgttgccgg acggggtgaa
     3361 aggggaaaac acct
//
