LOCUS       NZ_CP064670             4018 bp    DNA     circular CON 12-JAN-2024
DEFINITION  Salmonella sp. SJTUF14154 plasmid p14154D, complete sequence.
ACCESSION   NZ_CP064670
VERSION     NZ_CP064670.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15296096
            Assembly: GCF_015534775.1
KEYWORDS    RefSeq.
SOURCE      Salmonella sp. SJTUF14154
  ORGANISM  Salmonella sp. SJTUF14154
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4018)
  AUTHORS   Zhang,Z., Shi,C. and Shi,X.
  TITLE     Prevalence and Evolution of high drug-resistance Salmonella Indiana
            in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4018)
  AUTHORS   Zhang,Z., Shi,C. and Shi,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUN-2020) MOST-USDA Joint Research Center for Food
            Safety, Shanghai Jiao Tong University, Dongchuan RD800, Shanghai
            200240, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SOAPdenovo v. 2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 24x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/12/2024 03:08:51
            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)                     :: 4,823
            CDSs (total)                      :: 4,705
            Genes (coding)                    :: 4,535
            CDSs (with protein)               :: 4,535
            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)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 63 of 170
            Pseudo Genes (incomplete)         :: 130 of 170
            Pseudo Genes (internal stop)      :: 32 of 170
            Pseudo Genes (multiple problems)  :: 48 of 170
            Pseudo Genes (short protein)      :: 1 of 170
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP064670.1.
            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..4018
                     /organism="Salmonella sp. SJTUF14154"
                     /mol_type="genomic DNA"
                     /strain="SJTUF14154"
                     /isolation_source="Chicken meat"
                     /db_xref="taxon:2745893"
                     /plasmid="p14154D"
                     /geo_loc_name="China:Shandong"
                     /lat_lon="37 N 117 E"
                     /collection_date="2017"
                     /collected_by="Shanghai Jiao Tong University"
     gene            join(3706..4018,1..11)
                     /locus_tag="IVP16_RS23895"
                     /old_locus_tag="IVP16_23895"
     CDS             join(3706..4018,1..11)
                     /locus_tag="IVP16_RS23895"
                     /old_locus_tag="IVP16_23895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_024191642.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>654
                     /locus_tag="IVP16_RS24255"
                     /pseudo=""
     CDS             220..>654
                     /locus_tag="IVP16_RS24255"
                     /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            689..1174
                     /locus_tag="IVP16_RS23905"
                     /old_locus_tag="IVP16_23905"
     CDS             689..1174
                     /locus_tag="IVP16_RS23905"
                     /old_locus_tag="IVP16_23905"
                     /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_061390563.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1178..1393
                     /locus_tag="IVP16_RS23910"
                     /old_locus_tag="IVP16_23910"
     CDS             1178..1393
                     /locus_tag="IVP16_RS23910"
                     /old_locus_tag="IVP16_23910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_072048928.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1522..2049
                     /locus_tag="IVP16_RS23915"
                     /old_locus_tag="IVP16_23915"
     CDS             1522..2049
                     /locus_tag="IVP16_RS23915"
                     /old_locus_tag="IVP16_23915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016246513.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            2304..2516
                     /locus_tag="IVP16_RS23920"
                     /old_locus_tag="IVP16_23920"
     CDS             2304..2516
                     /locus_tag="IVP16_RS23920"
                     /old_locus_tag="IVP16_23920"
                     /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_034169353.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(2945..3058)
                     /locus_tag="IVP16_RS24330"
     CDS             complement(2945..3058)
                     /locus_tag="IVP16_RS24330"
                     /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_072035093.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     Typing          3416..3593
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          complement(2946..3466)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.564"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2..1485
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3707..4017
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.231"
                     /coverage="97.0"
                     /evalue="1.14e-59"
ORIGIN
        1 atgatcgtta agtttcatcc cagaggccgc ggcggtggcg gcggtccggt ggattatctg
       61 ctggggaaag accggcagcg cgacggcgcc agcgttctgc agggtaagcc ggaggaagtg
      121 cgggagctta ttgacgcctc gccttacgcc aagaaataca cctccggcgt gctgtctttt
      181 gccgaacagg atttgccgcc cggccagcgt gaaaagctga tggcgagctt tgagcgggtt
      241 ctgatgcccg gactcgataa agaccagtac agcgtactgt gggttgagca ccgggacaaa
      301 gggcggctgg agctgaactt cctgatcccg aacacggagc tgctgaccgg cagacgtctc
      361 cagccgtatt acgaccgcgc cgaccgtccg cgcattgatg cctggcagac catagtgaac
      421 ggcagactgg ggctgcacga cccgaacgcg ccggaaaacc ggcgggcgct ggttacaccg
      481 tccgcgctgc cggaagcgaa gcaggaagcc gcccaggcga ttacgcgcgg cctactttcc
      541 cttgcctcat ccggggagct gaaaacccgt caggacgtca ctgaggcgct ggaaagtgcg
      601 ggttttgagg tggtgcgcac cacgaaaagc agcatcagca ttgccgaccc tgacgggggg
      661 cgaaacatcc gactgaaggg agccatctat gaacagtctt ttaacgctgg cgaaggactt
      721 agagcagaaa tcgaaagcgc agcagcagac taccggcgag atgctgaaag ccgcattcag
      781 cgagcacgag aagtctgtca gagcggaact gagcgaaagc gagaagagaa tcagcgccgc
      841 catcctcgac cacgaccgga agctgtcctc agccatgagc caacgcacga aagggatgct
      901 gcgtatgatc agccagacgt ggctgaccat agtcctggtc tccgcgctac tgatcgcctc
      961 gagcgcgggc attctgtggt ggcaggggca acagatactc gacaactaca cgaccatcca
     1021 ggaacagaag agcacgcagg ccatgctttc agagaagaac aacggcgtcc agctcacgac
     1081 ctgcggggag gagagacgcc gctgcgtgag ggtgaacccg gaagcgggaa gattcggaga
     1141 ggattcgagc tggatgatac tggcggggaa atagcacatg acggaactgg aaaaacagtt
     1201 gctgagcgca ttagagcagc tacagcagga ctactcgaaa aggctggacg agtgggagaa
     1261 cgccttcgcg gaatggcgga cgatgtctgg gcttatgcaa cgggagaacg cggcgctgag
     1321 cgagcgcgtc acgggcttga gcaggcaggt gcagagtttg agcgatcagc tgcgccgatt
     1381 gtcgcaaggc tgaatggcat cgaggcgcac cgggagcagg agcgcgcggc gcagcaccag
     1441 aaagcgctgg agctggaacg atcgcagcgg cagaaaggtt ttgagcttgg aatgtagtta
     1501 atcaatgaaa agggatgcgt tatgaaatgt ttctgggctt gctcagtctc ggtggttttg
     1561 gctatgtcat ttacagtcgc tgctgcggag aataacgaca acgttacata tacaaaaccg
     1621 tcagccggga gggacttata tcttacctgt aaaggttatc aggtgaaggg ggcatctgta
     1681 attaacgtcg agaaaccttc ttaccttgaa ggtactggtg agcaggttga atttgcaatc
     1741 attactcctg ttggtgcgtc tgacggactc aaggtctttt ttgattcatg gggtttttct
     1801 tcatttggat tgattgaaag ccatgtgatg catgagcact ggtctttagt tcatgttggg
     1861 gggcgtgctt cagtcaaagg tgaaaagatt gattattcat ttgtagataa ccagccacag
     1921 gaggggggga gctataaacc caaaacaggt gtgttcctgt acggctgcat gaactcggat
     1981 aaaagaccat cttgggtcga aaagatctac acaagaacag gtgtgtttcg agggggcata
     2041 gaagactaaa atactgctta cagcatgaaa atccattgaa cagagtgtca gttcatttcc
     2101 gtgcataact atgcataccg taagaactta cggggggcat ttatcggcgt ttttacgtgg
     2161 taagaggtgc tcttttgcgg ttcatggcgc agaacggtgc tgaggctgtc tgcggcggtg
     2221 cgaacaaggg atgttatggt aaataagagt gtcttttgga tattttaaat ctgttttttt
     2281 attaaattta atgggggcag aaaatggggg attttgagcg tacctttgga gctggtgctg
     2341 attttgatcg gataattgat gagaataaca gcgaatattt tcgagaagat cgccgaaaaa
     2401 ctaaaaattc aaaaaaaaaa ttctcttctt ttcaagatgc tttggtttgg gcgaaagcta
     2461 atcctggcaa aacgataata agatctccag acggtgtggg gtttattgaa aaatgaaaga
     2521 gtggattcac tgtaaaacaa cagtcatttt ttggacaaca ctgtctatat acgtactcat
     2581 atgtttcaca gtgtcgtatg ttggagtcta tgttacgtac gttgcagggc ctattttgtt
     2641 agttacaggc attcttgcat ggcttacgaa acctagctgt aatccaaagt gactgggcta
     2701 gacgaacttt atccccccat aaaacccgct tttttaaacg gatcttcttg agatcattca
     2761 tggagaatcg taatctctta gcactgtaaa cgaaaaaacc gcccagcaag gcggtttttt
     2821 cgaaggttct cagagcagca actctttgaa ccgaggtaac tggcttggag gagcacagtc
     2881 accaaaactt gtcctttcag tttagcctta accggcgcat aacttcaaga ctaactcctc
     2941 taaatcagtt accagtggct gctgccagtg gcgttttgtc gtgtctttcc gggttggact
     3001 caagtcgata gttaccggat aaggcgcagc ggtcggactg aacggggggt tcgtgcatac
     3061 agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga attagataaa
     3121 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
     3181 agggagctac cagggggaaa cgcctgggat ctttatagtc ctgtcgggtt tcgccaccac
     3241 tgatttgagc gtcagatttc gtgatgcttg tcaggggggc ggagcctatg gaaaaacggc
     3301 aacgccgcat cctttttccg ccctttctga ttgatttccg cttagtctct ttatccagcc
     3361 attcgtaagc tggcaacgcc cgccgcagtc tcacggcagg agcgcagcga ccgagtgagc
     3421 gaggaggcgt catttcaccg ggatctgcat ttcgcactta cgccccacag cagcattttc
     3481 tccctgccac atgaagcact ttcctgaatc cccactccga tttaccatgt taagccagta
     3541 tacactccgc tagcgctacg tgactggttc agggctgcgc cccgaaaccc gctgaaaagt
     3601 actgccgcgc cctgcgggct tgcccaacac cgctccggac aggaaaaaat ttcccgcccg
     3661 aaccggtgtt atccggagga tggtttggca gaaaagcgca acaaaatgct cactatgtgg
     3721 gtgacagaag acgagcaccg ccgacttctg gagcgctgtg agggtaaaca actcgcggcc
     3781 tggatgcgcc agatatgcct ggacgaaaag ccctcgcgtg ctggcaaact tccatccatc
     3841 tcgccggcgc tgcttcgtca gcttgccggc atgggtaaca acctcaacca gattgcccgg
     3901 caggttaacg ccggtggcgg tactgggcac gatcgcgtgc aggttgtcgc cgtgctgatg
     3961 gccattgatg ccggactcga gcggctgcgg cacgccgtgc tggaaaaggg ggcagacg
//
