LOCUS       NZ_CP047534             4074 bp    DNA     circular CON 25-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            SJTUF10484 plasmid unnamedC, complete sequence.
ACCESSION   NZ_CP047534
VERSION     NZ_CP047534.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN09759462
            Assembly: GCF_004324025.2
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4074)
  AUTHORS   Shang,D., Zhao,H., Chang,J. and Shi,C.
  TITLE     Salmonella enterica subsp. enterica serovar Typhimurium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4074)
  AUTHORS   Shang,D., Zhao,H., Chang,J. and Shi,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JAN-2020) School of Agriculture and Biology, Shanghai
            Jiao Tong University, 800 Dongchuan Road, Minhang District,
            Shanghai, Shanghai 201100, China
REFERENCE   3  (bases 1 to 4074)
  AUTHORS   He,Y., Zhao,H., Zhang,Z., Zhou,X., Shi,C. and Shi,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-AUG-2018) School of Agriculture and Biology, Shanghai
            Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SOAPdenovo v. 2.04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004324025.2-RS_2024_05_25
            Annotation Date                   :: 05/25/2024 04:59:49
            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)                     :: 5,112
            CDSs (total)                      :: 4,987
            Genes (coding)                    :: 4,878
            CDSs (with protein)               :: 4,878
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 31 of 109
            Pseudo Genes (incomplete)         :: 90 of 109
            Pseudo Genes (internal stop)      :: 18 of 109
            Pseudo Genes (multiple problems)  :: 27 of 109
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047534.1.
            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..4074
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="SJTUF10484"
                     /serovar="Typhimurium"
                     /isolation_source="Clam"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="unnamedC"
                     /geo_loc_name="China: Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2007"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(477..731)
                     /gene="mobC"
                     /locus_tag="DXN09_RS25500"
                     /old_locus_tag="DXN09_025395"
     CDS             complement(477..731)
                     /gene="mobC"
                     /locus_tag="DXN09_RS25500"
                     /old_locus_tag="DXN09_025395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            910..3069
                     /gene="mobQ"
                     /locus_tag="DXN09_RS25505"
                     /old_locus_tag="DXN09_025400"
     CDS             910..3069
                     /gene="mobQ"
                     /locus_tag="DXN09_RS25505"
                     /old_locus_tag="DXN09_025400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_084568118.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRTERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREVPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(3327..4019)
                     /locus_tag="DXN09_RS25510"
                     /old_locus_tag="DXN09_025405"
     CDS             complement(3327..4019)
                     /locus_tag="DXN09_RS25510"
                     /old_locus_tag="DXN09_025405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(733..909)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          910..1268
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          complement(3328..4019)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          824..3066
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.064"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtggaatatt tttttttata tcctcacatt tctgtgaata acaccttaaa ttcctccacc
       61 tttaccttaa attcctccac ctaaacacct taaattcctc cacatatacc ttaaattcct
      121 ccacatatac cactgcaaca tattgatttt attaatgaat ttcgccccta aaacaagtat
      181 taaaaacaag atcttaaaaa caagatctaa aaacttaacg gcgagcctgt ggataacttg
      241 gggtgctgaa aacaaaaaac aaataaaaac aatgtgttgc aagaaagtag aattgcaagt
      301 tccgaatact ccccttccaa ccctgtggaa atccagtatt catgcgggtt cagcgcatat
      361 cacctgccga aaaaccgtgc gtatgtgctc aacctggcga cggattcact tccgcttcct
      421 cgcccactcg ctcgctaacg ctcggtcgct ggggctgcgg cgagcggacg atacaatcac
      481 tgtcctggca gcgcctccag ctcgttaatc agcggcagta tgcgcgtcac atcagcctgt
      541 cgtgtcacct ctgccttcag gaactggagt aaccaggcac gcaactgcac ctcctccggc
      601 tttctgacct ttgccagcaa tgctgcaccc acaacaacct tctgcgctgt gtccaagctc
      661 cggctcttcg ccttcaggcg ctgtaatctc gcctcagcat cagcaatctt ctgttcgagc
      721 gttctgctca tgatgtaact ccgtgcgcga tgaaaaatcg cattttagcg cgtcactggt
      781 agtttaaaaa ctgagctggc ataatgcacg gcaaatcacg aagtgcgcac ttatacaatc
      841 tccactccgt ttcgattgtg tgcgccctgc ggggctgaaa gaaaactaca aaaaggcatt
      901 acggcagaaa tggcgattta tcatctcagc atgaaaatta tctccagaag cagcggctac
      961 agcgccgtag cttccgctgc ctatcgttcc ggttcactga tgcttgatga gcgtaccgga
     1021 ctgactcacg actacacccg caaaagcggt gtggctgaag ctgtgattct gacccccgcg
     1081 acagcccctg cctggtgtac gaaccgtgcc gaactctgga atgccgttga gaaggccgaa
     1141 cgccggaaga actcacaact tgcgcgggaa attgaactcg ctatcccccg tgaactgccg
     1201 caggatgccg cacgggaaac cgttctcgcc tttgtcagag aaaactttgt cagtcagggc
     1261 atgattgctg atgtggcgtt ccatcacatg gataaaacaa atccccatgc gcacatcatg
     1321 ctgaccacga gggctgtcgg acctgctggg ttcggcggaa aggtcaggga ctggaacgac
     1381 cggacacatg ccgagacgtg gcgtgcatca tgggctgacc atgcaaacag agcactggcg
     1441 aacgccggtt atcaggaaga gatagaccat cgttcatacg agcgacaggg gcttgagaaa
     1501 acgcctggta ttcacctcgg aaagtctgcc tgtgcgatgg aaacacgcgg tatcgaaaca
     1561 gaacgcggcg aacagaatcg tctgattaac aggcttaacc tggaaataca gatttcccgc
     1621 actgaactca ggaacagcgg gctgacagag cctgcccgcc gtgtggctga ccttctgaat
     1681 atcgtgcttc ctgacaacgc aacttcgtac acactacgtg acatcatcga agcgttgccg
     1741 aaggacagta atgcggcatg gaaactcacc agtaatgcca tgtcgatgat ggcagatatg
     1801 caggcgacgc gcagacgctg ggaagagctg aacaccgaac gaaaggaagc gatgagccat
     1861 gctgccagcc tgaaaaaatc atcaccgttt tcgtccggtt tttcccgtat tcccctgatg
     1921 caatgggcgg caccggaata ccgtagcgaa cagggaaaaa ttcagtcgct gagccagcaa
     1981 atggaaaaat tgcgacagca ttaccggaag gtggagaaac aggacattcc cgcgagtcag
     2041 acggcatttg aaaaacagtg gcagcagtgg ggggcatccg gccttgcagc tctcagagtc
     2101 cagttgctta aacgtgaaga ggaattgcgc cggaaggagc aggaggatac agaacgtagt
     2161 cgcacggagc gacgagcgga acagctcagg aaaaatgaca atgccgttat ggattcaggg
     2221 gtactgagcg cagtcgttac ggggtatggc gaggccccca tgcctggtaa cggggaaatg
     2281 acctgttacc ttctgcttca caaccggaac ggagaataca cgctctgggg gaacgagctg
     2341 gagaaatacc gcaccagaat ctttgagcgt gttgatttaa tgcgtgacag gagtggttat
     2401 atctgtgacc gaagcgaaat cggtcaacat ccaccactgc aacgtgttta ttcctctgcg
     2461 acctttgagc aacttctgac gcaggtttgc cagacatggc cgcaatatac ccgcaatctc
     2521 cgccagccga agacatggcc ggagtctttc tgtcttggag aagaccgcca gccagccatg
     2581 ccatcactgg cagcaaggaa ggtggatttt acgcagggac gtctgccacc gacgctgatg
     2641 ccggtaatga gttctgtcga ccgggaaacc cgccagcttc agcttttgct ggtcatgggc
     2701 gtggatgact ctctgggcgg tgttgtccgg cttaatggta cgctgtatcc cgcgtttgcc
     2761 gttccctcag ccgataacag ccagctggtc atcagtgcac tgaccgataa ggggttacgg
     2821 tatgcagggt atggtgttgc cgtaaatcac gatgcagaca gccacatatc acctgcgccg
     2881 gaacttatgg agtttcatct gaaaacccgt gaggtaccgc tttttgctgc cgtcaacaca
     2941 ccagaaaaac agccggatca tctgttccgc tcgctgggtt tcaatcgtac ctgggacgaa
     3001 tggcggcgcg aggaagatgc aagaacacac accaccgaga ggagacatga tcgcggttgg
     3061 tcacagtgaa tgtgaacaat attttgtttt gtttaacatc gtgttatgtt cgttgatgtt
     3121 cttcgatgtt catcgacagg gatgaatgca agaagcacac tcacataacg caagcatagt
     3181 tttgtttttc cgcccccaaa aattgggggt tcttttttcg ctgcatcaga gcgtttttgg
     3241 cgcaattttt cacttcaata gtaccttcgc actactaaca caaaaaaaac gcagcaggga
     3301 gcgttttagg tgccttaaaa tcgattttag atcgtcatct tgatctgttt gtcttccttg
     3361 aagcgaaaat gcagggctac aaccgtgcgc ccctttttga tcgtctcaac cgttacagcc
     3421 aggtcgcttt ttttgttcag ttcgtcaaca cagggtttta ttagtatttt atttaagtct
     3481 ctgaattgtt tgtatttatt ttcaatccct aacattgaac gaaagtcatt aagagcaata
     3541 attctctctc ccgtactgcg gaattgctgg aggaactcgt atattcttat actgtaacta
     3601 cttgataaac ctgatatgtt ttttataaca acgcgcgtga attgcccctt cagttgcgtc
     3661 agataaggca ttaccgcgtc agaaaaggtt attcgagcct tggcctcacc tttagcgtac
     3721 tgtgcccgat actggatcca gcggaactcc tcacgcttct cgtcattctt gagaatgatc
     3781 gacctgtccc ataaacgatc gatcgcttcc tgtaactgaa cctcggcatt tttccgcccc
     3841 atgtcaggga atgaatcaaa atattccgca gcggtaatgg tcattgtctt ttgcaattca
     3901 gcatcagcac cagatttcaa tcgactgata cacagcaaca gaaaacgttg ttcctgtagg
     3961 gtcaacttgt agctggcctc aaccaaagca ttcgacttgt aggcaatcaa gtccgacata
     4021 caaagatccc gttcaaatgt ggtgatgctt taatgtgccc cacaaataag aaat
//
