LOCUS       NZ_CP045948             4251 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            AUSMDU00010530 plasmid pAUSMDU00010530_01, complete sequence.
ACCESSION   NZ_CP045948
VERSION     NZ_CP045948.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13191648
            Assembly: GCF_009664575.1
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 4251)
  AUTHORS   Baines,S.L., Goncalves da Silva,A., Carter,G.P., Jennison,A.V.,
            Rathnayake,I.U., Graham,R.M.A., Sintchenko,V., Wang,Q.,
            Rockett,R.J., Timms,V.J., Martinez,E., Ballard,S., Tomita,T.,
            Isles,N., Horan,K.A., Pitchers,W., Stinear,T.P., Williamson,D.A.,
            Howden,B.P. and Seemann,T.
  TITLE     Complete microbial genomes for public health in Australia and
            Southwest Pacific
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4251)
  AUTHORS   Baines,S.L., Goncalves da Silva,A., Carter,G.P., Jennison,A.V.,
            Rathnayake,I.U., Graham,R.M.A., Sintchenko,V., Wang,Q.,
            Rockett,R.J., Timms,V.J., Martinez,E., Ballard,S., Tomita,T.,
            Isles,N., Horan,K.A., Pitchers,W., Stinear,T.P., Williamson,D.A.,
            Howden,B.P. and Seemann,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2019) University of Melbourne, Microbiological
            Diagnostics Unit, First Floor, Building 248, Parkville, Victoria
            3010, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 03-JAN-2019
            Assembly Method                   :: Unicycler v. 0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 370x
            Sequencing Technology             :: PacBio RSII, Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:13:56
            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)                     :: 4,876
            CDSs (total)                      :: 4,756
            Genes (coding)                    :: 4,647
            CDSs (with protein)               :: 4,647
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 34 of 109
            Pseudo Genes (incomplete)         :: 87 of 109
            Pseudo Genes (internal stop)      :: 17 of 109
            Pseudo Genes (multiple problems)  :: 27 of 109
            Pseudo Genes (short protein)      :: 1 of 109
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045948.1.
            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..4251
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="AUSMDU00010530"
                     /serovar="Typhimurium"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pAUSMDU00010530_01"
                     /geo_loc_name="Australia"
                     /collection_date="2017"
     gene            complement(join(4251,1..113))
                     /locus_tag="GJE12_RS24665"
     CDS             complement(join(4251,1..113))
                     /locus_tag="GJE12_RS24665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_059446996.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERHDKAPLAAATGN"
                     /name="hypothetical protein"
     gene            755..1078
                     /locus_tag="GJE12_RS24220"
                     /old_locus_tag="GJE12_24220"
     CDS             755..1078
                     /locus_tag="GJE12_RS24220"
                     /old_locus_tag="GJE12_24220"
                     /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_179133778.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRQAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1287..>1721
                     /locus_tag="GJE12_RS24580"
                     /pseudo=""
     CDS             1287..>1721
                     /locus_tag="GJE12_RS24580"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            1756..2253
                     /locus_tag="GJE12_RS24230"
                     /old_locus_tag="GJE12_24230"
     CDS             1756..2253
                     /locus_tag="GJE12_RS24230"
                     /old_locus_tag="GJE12_24230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001086853.1"
                     /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_143549827.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELNESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQML
                     DNYTSIREQKDALEKLNARTWGVRYQEDNQGRFLVLPEGVKADTNWTFDNGRKNGIRLV
                     QE"
                     /name="MbeB family mobilization protein"
     gene            2260..2475
                     /locus_tag="GJE12_RS24235"
                     /old_locus_tag="GJE12_24235"
     CDS             2260..2475
                     /locus_tag="GJE12_RS24235"
                     /old_locus_tag="GJE12_24235"
                     /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_063617430.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSNG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2842..3339)
                     /locus_tag="GJE12_RS24240"
                     /old_locus_tag="GJE12_24240"
     CDS             complement(2842..3339)
                     /locus_tag="GJE12_RS24240"
                     /old_locus_tag="GJE12_24240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019842774.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_084567316.1"
                     /translation="MKKQILALALLSLPLIGMAKDSGYGNTEWGMTPNQVVAAQKGKAH
                     LIPPQKYKDQWGKVSIEDVNIGSGIYTVTFIFDASDKLVQTNVASKEKKNEGIANDQFN
                     LLNQLLTQKYGKPQFVSDEKATWKTDATTIELNKMIISGIMAQTLVRYIPNKTVISDTS
                     NL"
                     /name="hypothetical protein"
     gene            complement(3349..3936)
                     /locus_tag="GJE12_RS24245"
                     /old_locus_tag="GJE12_24245"
     CDS             complement(3349..3936)
                     /locus_tag="GJE12_RS24245"
                     /old_locus_tag="GJE12_24245"
                     /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_059337246.1"
                     /translation="MIRKIFFASAIVVAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTPLQLGAIWSSAYPDEAGLILSYNSNVSSGNAAYLGLTGIDINVDG
                     KISSYKAQQQTNLSSSSYNSVSKTIYTSSKNTIVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFLAKVERFK"
                     /name="hypothetical protein"
     Typing          468..646
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.011"
                     /coverage="83.0"
                     /evalue="3.460000000000001e-56"
     Typing          complement(2..492)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.165"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          1069..2579
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.071"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagttaccag tggctgctgc cagtggcgct ttgtcgtgtc tttccgggtt ggactcaaga
       61 tgatagttac cggacaaggc gcagcggtcg gactgaacgg ggggttcgtg catacagtcc
      121 agcttggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag ataaacgcgg
      181 ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga
      241 gctaccaggg ggaaacgcct gggatcttta tagtcctgtc gggtttcgcc gccactgatt
      301 tgagcgtcag atttcgtgat gcttgtcagg ggggcggagc ctatggaaaa acggcagcgc
      361 cgtatccttt ttccggcctt tcctgacttg agtgccatct ctttatcttg tcattcgtga
      421 gcaggtaacg cccgccgcag cctcacggca ggagcgtagc gaccgagtga gcgaggaggc
      481 gtcatgtcac cgttacctgc attttgcact tacgccctat agccgcattt tcccttgcaa
      541 catgaataac ttccctgaat taccactccg atctaacata ttcagccagt atacactccg
      601 ctagcgctac gtgactggtt cagggctgcg ccccgaaacc cgctaaaagc cactgacgcg
      661 cctgcggctt gtccaacacc acgccgttcg ggaaaaaatt tcccgcccgt cccggcgtta
      721 tcaggaggac agattggcag acaaacgcag caaaatgctc acgatgtggg taacggaaga
      781 cgagcaccgg cgtctgctgg agcgctgcga cggtaagcag ctcgcagcct ggatgcggca
      841 gacgtgtctg gacgaaaagc cggctcgcgc cggcaaactt ccctcgatct cgccggcgct
      901 gcttcggcag cttgccggca tgggtaacaa cctcaatcag attgccaggc aggttaacgc
      961 cggtggcggc agcgggcacg accgcgtgca ggtggtcgcc gcgctgatgg ccatcgatgc
     1021 cggactcgaa cggcttcgcc aggcagtgct ggaaaagggg gcagacgatg atcgttaagt
     1081 ttcatcccag agggcgcggc ggcggcgccg gtccggtgga ttatctgctg ggtaaagacc
     1141 ggcagcgcga cggcgccagc gttctgcagg ggaagccgga ggaagtccgg gagcttattg
     1201 acgcctcgcc ctacgccaaa aagtacacct ccggcgtgct gtcctttgcg gaacaggatt
     1261 tgccgcccgg ccagcgtgaa aagctgatgg cgagcttcga gcgggttctg atgcccgggc
     1321 tcgacaaaga tcagtacagc gtgctgtggg ttgagcacca ggacaaaggg cggctggagc
     1381 tgaacttcct catcccgaac acggagctgc tgaccggcaa acggctccag ccgtattacg
     1441 atcgcgccga ccgtccgcgc atcgacgcct ggcagaccat agtgaacggc aggctggggc
     1501 tgcacgaccc gaacgcgccg gagaaccggc gggcgctggt cacgccgtcc gcgctgccgg
     1561 aagcgaagca ggaagccgcc caggtgatta cgcgcggcct gcttgccctt gcctcagccg
     1621 gggagctgaa aacgcgccag gacgtcaccg aggcgctgga aaacgcaggt ttcgaggtgg
     1681 tgcgcaccac gaaaagcagc atcagcattg ccgacccgga cggggggcga aacatccgac
     1741 tcaggggagc catctatgaa cagtctttta acgctggcga aggacttaga gcagaaatcg
     1801 aaagcgcagc agcagactac cggcgagatg ctgaaagccg cattcagcga gcacgagaag
     1861 tctgtcagag cggaactgaa cgaaagcgag aagagaatca gcgccgccat cctagaccac
     1921 gaccggaagc tgtcctcagc catgagccag cgcacgaaag ggatgctgcg gatggtcagc
     1981 cagacgtggc tgaccatcgt cctggtctcc gcgctgctga tagcctcgag cgcgggcatt
     2041 ctgtggtggc aggggcagca gatgctcgac aattacacga gcatccggga gcagaaggac
     2101 gcgctggaga agctgaacgc gcggacgtgg ggcgtgaggt atcaggaaga caaccagggg
     2161 cgttttctgg tgctgccgga aggcgtgaaa gcggacacga actggacgtt cgacaacggc
     2221 aggaagaacg gcatcagact ggtgcaggag tagagcagca tgacggagct ggaaaaacag
     2281 ttgctgagcg cattagagca gctacagcag gactactcga aaaggctgga cgagtgggag
     2341 aacgccttcg cggaatggcg gacgatgtct gggcttatgc aacgggagaa cgcggcgctg
     2401 agcgagcgcg tcacgggctt gagcaggcag gtgcagagtt tgagcgagca gctgcgccgg
     2461 ttgtcgaacg gctgaatgcc gtcgagctgc atcagcagca ggagcgcgcg gcgcagcatc
     2521 agaaagcgct ggagctggag cgatcgcagc ggcagcggac gtataacggc ccgtcgctgt
     2581 gataaccgga taaaacgggg ctttcggcgg gtatctgcgc tgaaaacctg agccattcac
     2641 ccggctgcat ggctatgcag tccggggaaa tttaccggac gcaaacgggg cggtttaccg
     2701 ggcgctttgc tgcgggtttt accaagcagg caccgtattc acgccgaacc tgcccggagc
     2761 ggtgcgggca agagatgtta tgttcaatct cccacctcag atatagaaac aggagagaga
     2821 cactcagtga ggctacaatt attacaggtt agacgtgtca gaaatcacgg tcttattagg
     2881 aatgtagcga actagtgttt gagccataat tccggagatg atcatcttat ttagctcaat
     2941 tgttgtagca tcagttttcc atgttgcttt ttcatcactt acaaactgtg gtttgccgta
     3001 cttctgtgta agtaattgat ttaataagtt aaattggtcg ttcgctattc cctcgttttt
     3061 cttttctttg ctggcaacgt tggtttggac taatttatct gatgcgtcaa aaataaacgt
     3121 aactgtatat attccactac ctatattcac gtcttcaatg ctcacttttc cccattggtc
     3181 tttatacttt tgagggggga ttaaatgagc ttttcctttc tgggctgcaa cgacctgatt
     3241 tggggtcata ccccattcgg tattgccata accagagtcc tttgccatgc caatcagtgg
     3301 cagtgatagc aaagcgagtg caagaatctg cttcttcatg acgcctcctt atttaaaacg
     3361 ttcgactttg gccaggaact ctttaatgga aacgatcgct gtcgctttac ctccggggat
     3421 actttgtgct gagaagtcga tgtcttgatt tccttggctt gtgtgtatgc gaatgcggca
     3481 gtttttagct gataccatgc tctccagcaa tttatacggg ataacgatag tattcttgct
     3541 agaggtatag atcgtcttgg atacggagtt atatgagctg ctgcttagat tagtttgttg
     3601 ctgtgcttta tagctggata ttttaccatc aacatttata tcaatccccg tcaaacctaa
     3661 gtatgcggca tttccgctag atacattcga gttgtaggaa aggattagtc cagcctcatc
     3721 tggataggca ctagaccata tcgcgcccaa ctgaagtggt gttccccaag tgctgttagg
     3781 atcgtatagc gaatttggag atacctctat gacagtcgag ttatcaaagg ttgatgtttg
     3841 ctgagaaaca acacccattc ccgccaattt atccattgct gtacagccag agatcgctac
     3901 tacgatcgca gaagcaaaaa aaatcttcct tatcatttcg ttatcctatt tttttctttt
     3961 taacagagac tgaaaaaaac atcgtattcc cgaaaccatt ttgcacacga tattcttttt
     4021 taaaaggatt ttgaaaggat gcgggcagat cttcttgaga tccttaagcg agagtcgtaa
     4081 tctcttgacc acgaaacgaa aaaaccgccc tgcaaggcgg tttttcgaag gttctcagag
     4141 ctaccaactc tttgaaccga ggtaactggc ttggaggagc gcagtcacca aaacttgtcc
     4201 tttcagttta gccttaaccg gcgcataact tcaagactaa ctcctctaaa t
//
