LOCUS       NZ_CP040670             3208 bp    DNA     circular CON 25-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            SA20082869 plasmid pSA20082869.2, complete sequence.
ACCESSION   NZ_CP040670
VERSION     NZ_CP040670.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10833328
            Assembly: GCF_005954705.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3208)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Complete genome sequences of Canadian Typhimurium and I
            1,4,[5],12:i:-
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3208)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAY-2019) Public Health Agency of Canada, National
            Microbiology Laboratory at Guelph, 110 Stone Road West, Guelph,
            Ontario N1G3W4, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/25/2023 04:53:04
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,949
            CDSs (total)                      :: 4,829
            Genes (coding)                    :: 4,683
            CDSs (with protein)               :: 4,683
            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)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 58 of 146
            Pseudo Genes (incomplete)         :: 97 of 146
            Pseudo Genes (internal stop)      :: 23 of 146
            Pseudo Genes (multiple problems)  :: 31 of 146
            Pseudo Genes (short protein)      :: 1 of 146
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP040670.1.
            Bacteria and source DNA available from SA20082869.
            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..3208
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="SA20082869"
                     /serovar="1,4,[5],12:i:-"
                     /host="porcine"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="pSA20082869.2"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2008-06-17"
                     /collected_by="FNC/CIPARS"
     gene            1..816
                     /locus_tag="FGO77_RS24955"
                     /old_locus_tag="FGO77_24955"
     CDS             1..816
                     /locus_tag="FGO77_RS24955"
                     /old_locus_tag="FGO77_24955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="WP_000018330.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(1922..2116)
                     /locus_tag="FGO77_RS24965"
                     /old_locus_tag="FGO77_24965"
     CDS             complement(1922..2116)
                     /locus_tag="FGO77_RS24965"
                     /old_locus_tag="FGO77_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2400..2723
                     /gene="mobA"
                     /locus_tag="FGO77_RS24970"
                     /old_locus_tag="FGO77_24970"
     CDS             2400..2723
                     /gene="mobA"
                     /locus_tag="FGO77_RS24970"
                     /old_locus_tag="FGO77_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            <2968..>3063
                     /locus_tag="FGO77_RS25430"
                     /old_locus_tag="FGO77_24980"
                     /pseudo=""
     CDS             <2968..>3063
                     /locus_tag="FGO77_RS25430"
                     /old_locus_tag="FGO77_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     ARG             2..813
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2152..2391
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(1363..1887)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          2401..2720
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.32e-62"
ORIGIN
        1 atgagccata ttcaacggga aacgtcttgc tcgaggcagc gattaaattc caacctggat
       61 gctgatttat atgggtataa atgggctcgc gataatgtcg ggcaatcagg tgcgacaatc
      121 tatcgattgt atgggaagcc cgatgcgcca gagttgtttc tgaaacatgg caaaggtagc
      181 gttgccaatg atgttacaga tgagatggtc agactaaact ggctgacgga atttatgcct
      241 cttccgacca tcaagcattt tatccgtact cctgatgatg catggttact caccactgcg
      301 atccccggga aaacagcatt ccaggtatta gaagaatatc ctgattcagg tgaaaatatt
      361 gttgatgcgc tggcagcgtt cctgcgccgg ttgcattcga ttcctgtttg taattgtcct
      421 tttaacagcg atcgcgtatt tcgtctcgct caggcgcaat cacgaatgaa taacggtttg
      481 gttgatgcga gtgattttga tgatgagcgt aatggctggc ctgttgaaca agtctggaaa
      541 gaaatgcata agcttttgcc attctcaccg gattcagtcg tcactcatgg tgatttctca
      601 cttgataatc ttatttttga cgaggggaaa ttaataggtt gtattgatgt tggacgagtc
      661 ggaatcgcag accgatacca ggatcttgcc attctatgga actgcctcgg tgaattttct
      721 ccttcattac agaaacggct ttttcaaaaa tatggtattg ataatcctga tatgaataaa
      781 ttgcagtttc atttgatgct cgatgagttt ttctgatagt tagtctttaa tgaatgcggt
      841 tggcgcatcg gcgggcacct tgcgcgcgct gtcgctgttc atgccgcgca gcatgtcgat
      901 ggcatcgagc acacccttgt agctcctccg gggagaatca ggcgagcgac agatctctgc
      961 tctctgtcat cgagaagtat ggagatcaag aatgatgctt tgagagcctg ctgtatgcgt
     1021 gatgagttct acaaagatgg agtacttgta gccagaaggc ctcaggaatg gcgagctgtt
     1081 gccaatacca ggcaaagaag ggctagaagt cgttaggctt tgttgacgca gctagcgcaa
     1141 ggagattaat ctaactaggt tgaaaacgaa aaaaccgcct tggcgggcgg tttttcgaag
     1201 gttcatagag ttggcgctct ttgaaccgag gtaactggct ttgaggagca cagtcgccaa
     1261 aacttgttct ttcagtttag ccttatcagg tgcataactt caagactcaa ctcctctaaa
     1321 tcagttacca atggctgctg ccagtggcgt taagtcgtgt ctttccgggt tggactcaag
     1381 acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc
     1441 cagcttggag cgaacgacct acaccgaact gagataccaa cagcgtgagc tatgagaaag
     1501 cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac
     1561 aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg
     1621 gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct
     1681 atggaaaaac ggcatcggcg ctggcttgtt ccggtgcttt gctttttgct cacatgttct
     1741 ttccggcgtt atcccctgat tctgtggata accgtattac cgcctttgag tgagctgaca
     1801 ccgctcgccg cagtcgaacg accgagcgta gcgagtcagt gagcgaggaa gcggaagagc
     1861 gtctgacgtg gcattttctc cttacgctcc gctatgccgt tctgcatcct gtccgggtgc
     1921 gttatatccc ggtgcgattt tccgcttcaa agcgtgtctg tatgctgttc tgaagttctt
     1981 ccgcgagttc gtgcagcttc tcacacatgg cggcctgttc gtcagcatca agtgcgtcca
     2041 gtttttcgag cagcgtcagg ctctggcttt ttatgaatcc cgccatgttg agtacggttt
     2101 gctgctgctt gttcatcttt ctgttttctc cgttctttct gtcatctgcg ttgtgtgatt
     2161 atatcgagta ccacttttcg actgttttac cgccggtatt ctgctgtctg actctttgac
     2221 gggcatttct gtcagacaac actgtcactg ccaaaaaact gccgtgcttt tgtcggtaat
     2281 tcgagcttgc tgacaggaca ggatgtgcaa ttgttatacc gcgcatacat gcacgctatt
     2341 acaattaccc tggtcagggc tttgccccga cacccatgtc agatacggag ccatgtttta
     2401 tgacaaaacg aagtggaagt aatacgcgca ggcgggctat cagtcgccct gttcgtctga
     2461 cggcagaaga agaccaggaa atcagaaaaa gggctgctga atgcggcaag accgtttctg
     2521 gttttttacg ggcggcagct ctcggtaaga aagttaattc actgactgat gaccgagtgc
     2581 tgaaagaagt catgcgactg ggggcgttgc agaaaaaact ctttatcgac ggcaagcgtg
     2641 tcggggacag agagtatgcg gaggtgctga tagctattac ggagtatcac cgggccctgt
     2701 tatccaggct tatggcagat tagcttcccg gagggaaact gtcgaaaaca gacggtatga
     2761 acgccgtaag tccccaaacc gatcgccatt cactttcatg catagctatg cagtgagctg
     2821 aaagcaatcc tgacgcattt ttccggttta ccccggggaa aacatctctt tttgcggtgt
     2881 ttgcggcaga atcgcgttca gcgcgtttta gcggtgcgcg taatgagacg ttatggtaaa
     2941 tgggagcgtt agaaacagtc ccatttactt gatgccatgt tcctcgacta cgaagcggcc
     3001 aaagattatg cgacccgctc caggctggtc acggcggcga atatcccttc tttcggagcg
     3061 ccagaatgat gttggtctgg ccggattttc atatggcggg aaccacgttg tgtctcaaaa
     3121 tctctgatgt tacattgcac aagataaaaa tatatcatca tgaacaataa aactgtctgc
     3181 ttacataaac agtaatacaa ggggtgtt
//
