LOCUS       NZ_CP016867             3223 bp    DNA     circular CON 01-NOV-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium str. CDC
            2010K-1587 isolate USDA-ARS-USMARC-1908 plasmid pSTY4-2010K-1587,
            complete sequence.
ACCESSION   NZ_CP016867
VERSION     NZ_CP016867.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02716879
            Assembly: GCF_001623645.2
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium str. CDC
            2010K-1587
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium str. CDC...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovinia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     The Complete and Closed Genome Sequences of Ten Salmonella enterica
            subsp. enterica Serotypes Typhimurium Isolated from Human and Bovine
            Sources
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovinia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-AUG-2016) Meat Safety & Quality Research Unit,
            USDA-ARS U.S. Meat Animal Research Center, 844 Rd 313, Clay Center,
            NE 68933, United States of America
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: Celera v. 7.0
            Coverage                          :: 133.76
            Sequencing Technology             :: PacBio RS II C3 P5
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/01/2023 09:41:42
            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)                     :: 4,921
            CDSs (total)                      :: 4,799
            Genes (coding)                    :: 4,679
            CDSs (with protein)               :: 4,679
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 120
            CDSs (without protein)            :: 120
            Pseudo Genes (ambiguous residues) :: 0 of 120
            Pseudo Genes (frameshifted)       :: 41 of 120
            Pseudo Genes (incomplete)         :: 87 of 120
            Pseudo Genes (internal stop)      :: 20 of 120
            Pseudo Genes (multiple problems)  :: 26 of 120
            Pseudo Genes (short protein)      :: 1 of 120
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP016867.1.
            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..3223
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium str. CDC 2010K-1587"
                     /mol_type="genomic DNA"
                     /strain="CDC 2010K-1587"
                     /serovar="Typhimurium"
                     /isolate="USDA-ARS-USMARC-1908"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:1454641"
                     /plasmid="pSTY4-2010K-1587"
                     /geo_loc_name="USA: BIFSCo Region 8"
                     /collection_date="2006-06"
                     /collected_by="CDC"
     gene            complement(181..351)
                     /locus_tag="AX04_RS26000"
                     /old_locus_tag="AX04_24450"
     CDS             complement(181..351)
                     /locus_tag="AX04_RS26000"
                     /old_locus_tag="AX04_24450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     gene            990..1313
                     /locus_tag="AX04_RS26010"
                     /old_locus_tag="AX04_24455"
     CDS             990..1313
                     /locus_tag="AX04_RS26010"
                     /old_locus_tag="AX04_24455"
                     /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_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1522..>1956
                     /locus_tag="AX04_RS26670"
                     /pseudo=""
     CDS             1522..>1956
                     /locus_tag="AX04_RS26670"
                     /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            1991..2476
                     /locus_tag="AX04_RS26190"
     CDS             1991..2476
                     /locus_tag="AX04_RS26190"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2480..2695
                     /locus_tag="AX04_RS26195"
     CDS             2480..2695
                     /locus_tag="AX04_RS26195"
                     /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_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2863..3195
                     /locus_tag="AX04_RS26020"
                     /old_locus_tag="AX04_24465"
     CDS             2863..3195
                     /locus_tag="AX04_RS26020"
                     /old_locus_tag="AX04_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     ARG             2864..3195
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          703..894
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(240..720)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          1304..2793
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaggattt ccttgagatc ctttctttct gcgcgtaatc tttttccctg taaacaaaaa
       61 aaccaccgct accaacggtg gttcgtttgc cggaattcag agctaccaac tctttgttcc
      121 gatggtaact ggctttcacg gagcgcagat acctaaactg tcctttcagt gtagccgcac
      181 tcaggctttc acttcaagaa ctctgtaggc attctctaca atctctgctc cgtgaaccca
      241 gttaccaatg gctaccgcca ctggcgattt gtcgtgtctt tccgggttgg actcaagttg
      301 atagttaccg gaacgggcgt ggtagtcgga ctgaacgggg ggttcgtgca tacagtccat
      361 cctggagcga actgcctacc cggaaccgag tttcaggcgt ggaatgagaa accgcggcca
      421 taacagcgga atgacaccgg taaaccgaaa ggcaggaatg cgggggagca cgagggagcc
      481 accaggggga aacgcctggt atctttaagc cgcatcgggt ttcgccaccg ctgatttgag
      541 cgtcattttc gtgatactcg tcaggggggc ggagcctatg gaaaaacggc aactccgcat
      601 ccttttcttg gcctttcctg cttcgagcgg catttgctta tcccgtaatc tgtgagctgg
      661 taacgcccgc cgcagtctca cggcaggagc gtagcgaccg agtgagcgag gaggcgtcat
      721 ttcatcacca cctgcatttt gcacttacgc ccggcagccg catttttccc ctgtcacatg
      781 aagcactttc ataaattgcc actccgtcat aacatgttta gccagtatac actccgctag
      841 cgctacgtga ctggttcagg gctgcgcccc gaaacccgct aaaaccactg ccgcgcctgc
      901 ggcttgtcca acaccgtgcc gaccgggaaa agatttcccg tccgtcccgg cgttatcagg
      961 aggccggatt ggcagacaaa cgcagcaaaa tgctcaccat gtgggtgact gaggacgagc
     1021 accggcgtct gctggagcgc tgcgagggta agcaactcgc ggcctggatg cggcagacgt
     1081 gcctggacga gaagcccgca cgcgccggca aacttccgtc gatctcgccg gcgctgcttc
     1141 gtcagcttgc cggcatgggg aacaacctta accagattgc ccgccaggtt aacgccggtg
     1201 gtggaagcgg acacgaccgc gtgcagattg tcgccgcgct gatggccatc gatgccggac
     1261 tcgagcggtt gcggcatgcc gtactggaaa agggtgctga tgatgatcgt taagtttcat
     1321 cctcgggggc gcggcggcgg cggcgggccg gtcgattatc tgctgggtaa agatcgccag
     1381 cgcgacggcg ccagcgttct gcaggggaag ccggatgaag tccgggagct tatcgacgcc
     1441 tcgccctacg ccaaaaagta cacttccggc gttctgtctt ttgccgaaca ggatttaccg
     1501 cccggccagc gcgaaaagct gatggcgagt ttcgagcggg ttctgatgcc cggactcgat
     1561 aaagaccagt acagcgtgct gtgggttgag caccgggaca aggggcggct ggagctgaac
     1621 ttcctgatcc cgaacacgga gcttctgacc ggcaagcggc tacagccgta ttacgaccgc
     1681 gccgaccgtc cgcgcatcga tgcctggcag accatagtga acggcaggct ggggctgcat
     1741 gacccgaacg cgccggagaa ccggcgggtg ctggtctcgc cttccgcgct gccggaagcg
     1801 aagcaggaag ccgcccaggc gattacgagc ggcctgcttg cccttgcctc atccggggag
     1861 ctgaaaacgc gtcaggacgt cactgaggcg ctggaaagcg caggttttga ggtggtgcgc
     1921 accacaaaaa gcagcatcag cattgccgac ccggacgggg ggcgaaacat ccgactgaag
     1981 ggagccatct atgaacagtc ttttaacgct ggcgaaggac ttagagcaga aatcgaaagc
     2041 gcagcagcag actaccggcg agatgctgaa agccgcattc agcgagcacg agaagtctgt
     2101 cagagcggaa ctgagcgaaa gcgagaagag aatcagcgcc gccatcctcg accacgaccg
     2161 gaagctgtcc tcagccatga gccagcgcac gaaagggatg ctgcgcatgg tcagccagac
     2221 gtggctgacc atcgttctgg tctccgcgct gctgatagcg tcgagcgcgg gcattctgtg
     2281 gtggcagggg cagcagatac tcgagaacta tacgaccatc cgggagcaga agagcacgca
     2341 ggccatgctg tcagagagga acagcggcgt acagctctcg acctgcggcg agcagagacg
     2401 ccgctgcgtg agggtgaacc cggaagcggg acagttcgga gaggactcga gctggatgat
     2461 actggcgggg aaatagcaca tgacggagct ggaaaaacag ttgctgagcg cattagagca
     2521 gctacagcag gactactcga aaaggctgga cgagtgggag aacgccttcg cggaatggcg
     2581 gacgatgtct ggtcttattc aacgggagaa cgcggcgctg aacgagcgcg tcacggtctt
     2641 gagcaggcag gtgcagagtt tgagcgagca gctgcgccgg ttgtcgaaag gctgaacgcg
     2701 atagaaactc accggcagca ggagcgggcg gtgcagcacc agaaagcgct ggagctggaa
     2761 cgatcgcagt ggcagcatca tggtccttcg ctatgataag ccgggttcta ttaattagtt
     2821 gttatgtaaa gatatttaaa tttttcaaca tgaggtattt ttatgaatac atatattttc
     2881 ctgggagggg ctattgtggc tgaagtcata ggcaccacct ttatgaaata ttcagaagga
     2941 tttacacgcc tgtggccgtc tgtaggaact gcaataagtt attgcgctgc cttttatctg
     3001 ctttcccaaa cattggaaaa tatacctacc ggtattgctt acgcaatttg gtctggtgcg
     3061 ggaattgtac taataagcct agctggttgg ttggttagcg gtcaaaaact tgattggccc
     3121 gcaattgcag gaatgttcct tatttgcgtt ggagttttgg ttattaatat tttttcaaaa
     3181 tcttctgcgc attaactttt taccgaagca tattggccaa agc
//
