LOCUS       NZ_CP032499             5836 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain SO21
            plasmid pSO21_ColRNAI_5.8, complete sequence.
ACCESSION   NZ_CP032499
VERSION     NZ_CP032499.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10076455
            Assembly: GCF_009497855.1
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 5836)
  AUTHORS   Vinuesa,P., Silva,C., Calva,E., Zaidi,M.B. and Puente,J.L.
  TITLE     Evolutionary genomics of Salmonella Typhimurium ST213
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5836)
  AUTHORS   Vinuesa,P., Silva,C., Calva,E. and Puente,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-SEP-2018) Ingenieria Genomica, Centro de Ciencias
            Genomicas - UNAM, Avenida Universidad 2001, Cuernavaca, Mor. 62210,
            Mexico
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 30-AUG-2018
            Assembly Method                   :: unicycler v. 0.4.5
            Assembly Name                     :: SO21_hybrid_MinION_GAIIx
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 433x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/13/2023 03:16:39
            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)                     :: 4,970
            CDSs (total)                      :: 4,847
            Genes (coding)                    :: 4,734
            CDSs (with protein)               :: 4,734
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 113
            CDSs (without protein)            :: 113
            Pseudo Genes (ambiguous residues) :: 0 of 113
            Pseudo Genes (frameshifted)       :: 36 of 113
            Pseudo Genes (incomplete)         :: 85 of 113
            Pseudo Genes (internal stop)      :: 19 of 113
            Pseudo Genes (multiple problems)  :: 25 of 113
            Pseudo Genes (short protein)      :: 1 of 113
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP032499.1.
            Bacteria available from Claudia Silva, IBT-UNAM,
            csilvamex1@yahoo.com.
            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..5836
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="SO21"
                     /serovar="Typhimurium"
                     /isolation_source="retail meat"
                     /host="Beef"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pSO21_ColRNAI_5.8"
                     /geo_loc_name="Mexico: Sonora"
                     /lat_lon="29.09 N 110.95 W"
                     /collection_date="2004"
                     /collected_by="M. Zaidi"
                     /genotype="ST213"
     gene            294..419
                     /locus_tag="D5069_RS25170"
                     /old_locus_tag="D5069_25185"
     CDS             294..419
                     /locus_tag="D5069_RS25170"
                     /old_locus_tag="D5069_25185"
                     /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="replication initiation protein"
                     /protein_id="WP_071535512.1"
                     /translation="MHEPPVQSDCCALSGNYPLESKPERHDKAPLAAAIGNLVRR"
                     /name="replication initiation protein"
     gene            937..1452
                     /locus_tag="D5069_RS24645"
                     /old_locus_tag="D5069_25195"
     CDS             937..1452
                     /locus_tag="D5069_RS24645"
                     /old_locus_tag="D5069_25195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675352.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675353.1"
                     /translation="MKFYTISSSYIKYLKDFDDKVPNSEDPTYNNPKAFIGIVLEIEGH
                     KYLAPLTSPKAWHANVKESSPAFFKLHENGVPDNQLGLINLKFMIPIIEAEVSLLDLDS
                     MPDTPYKRMLYKQLQFIRVNEDKISEKSKLLRNLALQGRMQGTCDFAVLEEKYQHFGKK
                     PEDMEIDD"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            complement(1564..2274)
                     /locus_tag="D5069_RS24650"
                     /old_locus_tag="D5069_25200"
     CDS             complement(1564..2274)
                     /locus_tag="D5069_RS24650"
                     /old_locus_tag="D5069_25200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024177388.1"
                     /translation="MLYWKRMPSLWIGIKISEFNDLDTAKAIAALKIYLTFCLFCKESD
                     SGQRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNLSTTVRKKIYTIDVLEKHDD
                     GWCKLPFKGIVGEDGKISAFQSMHNRYPFELLALQTYMYLLYARDNRNEYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRIVKKSIENKPLEMFHDSCYFYFRAGSNSALTYKR
                     KSEVLNLSEEDLPF"
                     /name="hypothetical protein"
     gene            2819..3076
                     /locus_tag="D5069_RS24655"
                     /old_locus_tag="D5069_25205"
     CDS             2819..3076
                     /locus_tag="D5069_RS24655"
                     /old_locus_tag="D5069_25205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001508827.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001508827.1"
                     /translation="MPKKTSKPNDLSNTINNIKKEINSGFTELLNRVEALEASDAQHSM
                     AIRDLQIQARAARGDKRMDIARDFGLSEGRISQIVNAGRN"
                     /name="hypothetical protein"
     gene            3086..3367
                     /locus_tag="D5069_RS24660"
                     /old_locus_tag="D5069_25210"
     CDS             3086..3367
                     /locus_tag="D5069_RS24660"
                     /old_locus_tag="D5069_25210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000786945.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024177387.1"
                     /translation="MKNEDDYKTGWTTQTTNPATGKKCSGGAARNLRIYQAGGANSVRV
                     KAAIEGVQSIQPIIDMQQSQIEQQQTQIAMLTQSLSQAINELTKSRNQ"
                     /name="hypothetical protein"
     gene            complement(3680..3913)
                     /locus_tag="D5069_RS24665"
                     /old_locus_tag="D5069_25215"
     CDS             complement(3680..3913)
                     /locus_tag="D5069_RS24665"
                     /old_locus_tag="D5069_25215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_029401705.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3920..4438)
                     /locus_tag="D5069_RS24670"
                     /old_locus_tag="D5069_25220"
     CDS             complement(3920..4438)
                     /locus_tag="D5069_RS24670"
                     /old_locus_tag="D5069_25220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_043991090.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKGAIARFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4476..5126)
                     /locus_tag="D5069_RS25040"
                     /old_locus_tag="D5069_25225"
                     /pseudo=""
     CDS             complement(<4476..5126)
                     /locus_tag="D5069_RS25040"
                     /old_locus_tag="D5069_25225"
                     /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            complement(5116..5439)
                     /locus_tag="D5069_RS24680"
                     /old_locus_tag="D5069_25230"
     CDS             complement(5116..5439)
                     /locus_tag="D5069_RS24680"
                     /old_locus_tag="D5069_25230"
                     /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_001508824.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVVALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5504..5695
                     /locus_tag="D5069_RS24685"
                     /old_locus_tag="D5069_25235"
     CDS             5504..5695
                     /locus_tag="D5069_RS24685"
                     /old_locus_tag="D5069_25235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          116..633
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.792"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3604..5126)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.571"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cggaaagaac atgtgcgcaa aaggcaaagg ccgggagaaa ggccacgccg atggcgtttt
       61 tccataggct ccgcccccct gacgagcatc acaaaaaccg acgctcaagt cagaggtggc
      121 gaaacccgac aggacttaaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc
      181 tcctgttcct gccattcggt ttaccggtgt cactccgctg ttatggccgc gtttatctca
      241 ttccacgcct gacactcggt tccgggtagg cagttcgctc caagctggac tgtatgcacg
      301 aaccccccgt tcagtccgac tgctgcgcct tatccggtaa ctatccactt gagtccaaac
      361 cggaaagaca cgacaaagcg ccactggcag cagccattgg taacttggtt cgcagatgat
      421 ttgttagcta aacacgaggt tgctcttgaa gtgtgcgcct cagtacggct acactggaag
      481 gacagatttg gttgctgtgc tctgcgaaag ccagttacca cggtccagaa acttgccggt
      541 ttactgaacc ttcgaaaaaa ccaccttgcc gggtggtttt tccgttttca gaccaagaga
      601 ttacgcgcag aaaaagatga tctcaagaag atccttttga ttagtgccgt catttgactg
      661 aacatcccat gctaagcacc tagttgtaag cccaagcgaa gatcatgtat acttagttca
      721 aggtgatttg ctacctttaa gtgcagctag aaatttaggt gatttgctac ctttaagtgc
      781 agctagaaat tcaggtgatt tgctaccttt aagtgcagct agaaattcag gtgatttgct
      841 acctttaagt gcagctagaa atttaggtca tttactacct taaagtaata aagtaaaaaa
      901 ggcgactata cacagtcgcc ttttttacga gaaaaaatga aattttacac aatatcaagc
      961 agttacataa aatacctgaa ggactttgat gacaaagttc ccaatagcga agatcctaca
     1021 tacaacaatc ctaaggcttt cattggcata gtactagaga ttgaaggaca taaatattta
     1081 gcacctttaa catcgccaaa agcatggcat gctaatgtaa aagagtcatc acccgccttc
     1141 ttcaaacttc atgaaaacgg tgtccctgat aatcagcttg gattgattaa tctgaaattt
     1201 atgattccaa taatcgaagc tgaagtgtct ttacttgatc tggatagcat gcctgatacg
     1261 ccttacaaaa gaatgctata taaacagtta caatttattc gtgtaaatga agataaaata
     1321 tctgaaaaat caaaactatt aagaaacctt gccttgcaag gcagaatgca aggaacatgc
     1381 gactttgccg tgttagaaga aaaatatcaa catttcggta aaaaacctga agacatggaa
     1441 atagacgatt aaccattctt ttttatggaa ttgaaggtcc aaaatcaagc ggttttggac
     1501 ctattttttt tgctctcatc caatataaga atgagatatt ctaattttga tttcgagaag
     1561 caatcaaaaa ggcaagtcct cctctgaaag attaagcacc tctgatttcc ttttgtaagt
     1621 gagagcgctg ttacttcccg ctctaaagta gaagtaacat gaatcatgaa acatttccaa
     1681 cggcttgttt tctattgatt ttttaacaat cctatcaagt aaaccgatat gaataagata
     1741 ggtaatagct ttatttagtt caggtagttt gcatttcagt tttttacata ttgttttttt
     1801 cctggcaaga gtatactcat ttctattatc tcgagcataa agaaggtaca tgtaggtttg
     1861 taaagctagc aactcaaatg gatatctgtt gtgcatggat tgaaatgcac ttatttttcc
     1921 atcttcacct acaattcctt taaagggaag cttacaccaa ccatcatcat gcttctctaa
     1981 tacatctatg gtataaattt ttttacgtac tgtcgttgat aaatttttta tcaactcttt
     2041 tgcataaaga attttaagcc cttcgttaac taacgatcgg cttaatgatg ctatctcaca
     2101 taggttacta aaagttagct caacagttct ctgtcctgaa tctgactctt tgcagaaaag
     2161 gcaaaatgtt aaataaatct ttaacgcggc gatcgctttt gctgtatcaa gatcgttgaa
     2221 ttcagatatt ttgataccta tccatagtga aggcattctt ttccagtaca gcataaatca
     2281 cctcattccc agaatttgaa aaatgaaata gaccaacccc aatacagaca tagatagcac
     2341 cagattagtt agcaccactg cgaccttcgc aagcctttca gccaaaaaca cacctttctc
     2401 aaacattttt tatccctcct gatagctttg tttttttgat tatctcaggc tgtgaaggcg
     2461 ttgtaacgcc ttcacaaaaa tctatctaga aagataagat aaggcaaaag aaagatatct
     2521 atatgttata taagatattt tatcttgctt ttggtattct tagaaatcat attatggttc
     2581 atggtgaacc gtaaatgcag tgctgatgct tttctggtta cgttaaatgt tttcacatta
     2641 ggactttaga tcagaacaaa caaagcgttg tgccttgcaa gccaccctgc ataaagcact
     2701 aaatttcttt atctcattaa attcaccttg ccaaaaggag caataatccc taccttacaa
     2761 ctttaacaaa actaaaaatc tttagcggac ttagccgccg agtatagaga aatatgccat
     2821 gcctaaaaaa acatcaaaac caaacgattt aagcaacact atcaacaaca taaagaaaga
     2881 aattaactca ggttttactg agttacttaa tcgcgtagaa gccttagagg ctagtgacgc
     2941 acaacacagc atggcgatac gtgatttaca aattcaggct agagccgctc gcggagacaa
     3001 gcgcatggat atagcaagag actttggcct cagcgaggga cgaattagcc agatcgttaa
     3061 tgcgggtcgt aactaagaca gacttatgaa aaatgaagac gactacaaaa caggatggac
     3121 gactcagaca acaaacccgg caacagggaa aaaatgttct ggaggcgcag ccagaaactt
     3181 aaggatatat caagccggtg gagcaaactc cgtgcgggta aaagctgcaa tcgagggtgt
     3241 ccagtcaata cagccaatca tcgatatgca acagtcacaa atcgagcaac aacaaactca
     3301 aatagcaatg ctgactcaat ctttgtctca ggcaatcaat gagctaacaa aaagcaggaa
     3361 tcaataggct ataaaggatg ttatttacca taacatccgt tgcccgcacc gccccggaca
     3421 gcttcgccgc gaacggggcg gcagtcagcc aaaaccaaca acaaatcacc cgaaaagcta
     3481 ccgcgatcgc gcctgataaa ttttaaccgt atgaatatct atgcaaccag atggtgcaga
     3541 ctacattagc ccgtcaaaat ccactgaatc tgccattttt tatagtttcg ccatcacagc
     3601 gacaacgaag gaccatccag cgtgcgttcc cgttccaggg ataacgcatg ttcgcgctca
     3661 tgtatcaacc gttcctctct tatctccagt tctcgctgta taactggctc aagcgttctg
     3721 tccgctcgct caagtgctgc acctgctgac tcaactgcat gacccgctcg ttcagcatcg
     3781 cgttgtcccg ttgcgtaagc gaaaacatct tctgcaattc cacgaaggcg ctctcccatt
     3841 cgctcagccg ctgcatatag tcctgttgca gctgctctaa ggcgttcagc aaatgtgttt
     3901 ccagctctgt cactctgtat cactccttca gatgtaccca ttccttcccc tgaaaggaaa
     3961 tcacctctgc tgacttcccg taaggaagga ccagaaattt cctgttcccg tcctgcacaa
     4021 actccacgcc ccatgtcttc gcgttcagtt tctgtaatgt ctcttcctgc ttcctgatat
     4081 cttccaggtt cgcctgtatc ctcccgccaa gataccagag cgtcccgcca ctcgcggtaa
     4141 acaggagaaa gactatcccc agtaacatca tgcccgtatt ccctgccagc tttaacacgt
     4201 ccctcctgtg ctgcatcatc gcctctttca ccccttcccg gtgtttttcc agcgattcct
     4261 ccgtcgaggc cgtaaaccgg gctatagcgc ctttgatttt cgtctcgttt gaggtcacag
     4321 cctcgcttac agattcgcca agcctgctga attcgtcgtt cagcattttc tctgtagatt
     4381 cggctctctc tttcagcttt ttctcgaact ccgcgcccgt ccgtaaaaga ttgctcataa
     4441 aacgctcctt tcagtctgat attcctcccg ccgttcgggt ctgcaatgct gatactgctt
     4501 cgcgtcaccc tgaccacgtc aagccccgcc tctgtgagcg cctgaatcac atcctgacgg
     4561 ccttttatct ctccgtaatg gtaaagcacc tccagacctc gtgtaacgct ctcagcaagc
     4621 gcctgtttcg tttccggcag gttatcaggg agtgtcagcg tcctgcggtt ctccggggcg
     4681 ttggggtcat gcagcccgta atggtgattc accagcgtct gccaggcatc aattctcggc
     4741 ctgtctgccc ggtcgtagta cggctggagg cgttttccgc tctgtagctc catgttcgga
     4801 atgacaaaat tcagctcaag acgccccttg tcctggtgct ccacccacag aatgctgtac
     4861 tgattttttt cgagaccggg catcagtacg cgctcaaagc tctccatcac tttttcacgt
     4921 cctcccggcg gcagttcctt ctctgcgaac gacagaacac cggacgtgta tttcttcgca
     4981 aatggcgtgg catcaataag ctcccggact tcttccgggt taccctgaag taccgttgca
     5041 ccttcccggt tacgctccct ccccagaagg taatcaaccg gaccactgcc accacctttt
     5101 ccccgggcat gaaacttaac tatcatcccg cgctccctgt tccctgacga cctgtcgtaa
     5161 gctgcgcaac tctctctcga tggccatcag tgcgaccacc acctgaaccc ggtcgccgga
     5221 agaccactgc ccgctgttca ccttcctcgc cgtctgatta aggttattcc cgatggcagc
     5281 cagctgacgc agtaacggcg gtgccagtgt cggcagcttc ccggaacggg caaccggctc
     5341 acccaggcag acccgccgca tccataccgc cagttgttta ccctcacagc gttccagtaa
     5401 ccgggcatgt tcatcatcag taacccgtat cgtgagcatc ctctctcgtt tcatcggtat
     5461 cattaccccc atgaacagaa atccccctta cacggaggca tcagtgacta aacaggaaaa
     5521 aaccgccctt aacatggccc gctttatcag aagccagaca ttaacgctgc tggagaaact
     5581 caacgaactg gacgcggatg aacaggcaga catctgtgaa tctcttcacg accacgccga
     5641 tgagctttac cgcagctgcc tcgcacgctt cggggatgac ggtgaaaacc tctgacacat
     5701 acagctcccg gagacggtca cagcttgtct gtgagcggat gccgggagca gacaagcccg
     5761 tcagggcgcg tcagggggtt tcggggcgaa gccctgaacc agtcacgtag cgatagcgga
     5821 gtgtatactg gcttaa
//
