LOCUS       NZ_CP016866             4675 bp    DNA     circular CON 01-NOV-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium str. CDC
            2010K-1587 isolate USDA-ARS-USMARC-1908 plasmid pSTY3-2010K-1587,
            complete sequence.
ACCESSION   NZ_CP016866
VERSION     NZ_CP016866.1
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 4675)
  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  JOURNAL   Unpublished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 4675)
  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
            CP016866.1.
            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..4675
                     /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="pSTY3-2010K-1587"
                     /geo_loc_name="USA: BIFSCo Region 8"
                     /collection_date="2006-06"
                     /collected_by="CDC"
     gene            22..345
                     /locus_tag="AX04_RS25950"
                     /old_locus_tag="AX04_24420"
     CDS             22..345
                     /locus_tag="AX04_RS25950"
                     /old_locus_tag="AX04_24420"
                     /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_024143074.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            554..>988
                     /locus_tag="AX04_RS26665"
                     /pseudo=""
     CDS             554..>988
                     /locus_tag="AX04_RS26665"
                     /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            1023..1508
                     /locus_tag="AX04_RS26175"
     CDS             1023..1508
                     /locus_tag="AX04_RS26175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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_139136427.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1512..1721
                     /locus_tag="AX04_RS26180"
     CDS             1512..1721
                     /locus_tag="AX04_RS26180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014538403.1"
                     /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_014538403.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1818..2000
                     /locus_tag="AX04_RS25960"
                     /old_locus_tag="AX04_24430"
     CDS             1818..2000
                     /locus_tag="AX04_RS25960"
                     /old_locus_tag="AX04_24430"
                     /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_020833677.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            2303..2572
                     /locus_tag="AX04_RS25965"
                     /old_locus_tag="AX04_24435"
     CDS             2303..2572
                     /locus_tag="AX04_RS25965"
                     /old_locus_tag="AX04_24435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019080654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024143071.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            2587..2926
                     /locus_tag="AX04_RS25970"
                     /old_locus_tag="AX04_24440"
                     /pseudo=""
     CDS             2587..2926
                     /locus_tag="AX04_RS25970"
                     /old_locus_tag="AX04_24440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822260.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(3027..3614)
                     /locus_tag="AX04_RS25975"
                     /old_locus_tag="AX04_24445"
     CDS             complement(3027..3614)
                     /locus_tag="AX04_RS25975"
                     /old_locus_tag="AX04_24445"
                     /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_020833680.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     Typing          4409..4588
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          complement(3947..4426)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.309"
                     /coverage="92.0"
                     /evalue="2.1e-176"
     Typing          336..1831
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.585"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttggcagata aacgcagcaa aatgctcacg atgtgggtga cggaagatga gcacaggcgt
       61 ctgctggagc gctgcgaggg taaacagctc gcggcctgga tgcgccagac gtgcctggac
      121 gagaagcccg cacgcgccgg caaacttccc tcgatctcgc cggcgctgct tcgtcagctt
      181 gccggcatgg gaaacaacct caaccagatt gcccggcagg ttaacgccgg tggcggcagc
      241 gggcacgacc gcgtgcaggt tgtcgctgcg ctgatggcca tcgacgcagg actcgagcgg
      301 ctgcggcacg ccgtactgga aaaaggggca gacgatgatc gttaagtttc acccgagagg
      361 gcgcggcggc ggtgccggtc cggtggatta tctgctgggc aaagaccggc accgcgacgg
      421 cgccagcgtt ctgcagggga agccggagga agtccgggag cttatcgatg cctcgcctta
      481 cgccaaaaag tacacctccg gcgtcctgtc atttgccgaa caggacttac cgcccggaca
      541 gcgtgaaaag ctgatggcga gcttcgagcg ggttctgatg cccggactcg ataaagatca
      601 gtacagcgtg ctgtgggttg agcacaacga caaagggcgg cttgagctga atttcctgat
      661 accaaacacg gagctgctga ccggcaggcg tctccagccg tattacgacc gcgccgaccg
      721 tccgcgcatc gatgcctggc agaccatcgt gaacggtcgg ctggggctgc acgacccgaa
      781 cgcgccggag aaccggcggg cgctggccac gccgtccgcg ctgccggaaa cgaagcagga
      841 agctgcccag actattacgc ggggtttact ggccttagcc tcgtccgggg agctgaaaac
      901 gcgacaggac gtcactgagg cgctggaaaa cgcaggtttt gaggtggtgc gcaccacaaa
      961 aagcagcatc agcattgccg acccggacgg ggggcgaaac atccgactga agggagccat
     1021 ctatgaacag tcttttaacg ctggcgaagg acttagagca gaaatcgaaa gcgcagcagc
     1081 agactaccgg cgagatgctg aaagccgcat tcagcgagca cgagaagtct gtcagagcgg
     1141 aactgagcga aagcgagaag agaatcagcg ccgccatcct cgaccacgac cggaagctgt
     1201 cctcagccat gagccagcgc acgaaaggga tgctgcgcat ggtcagccag acgtggctga
     1261 ccatcgtgct ggtctccgcg ctgctgatcg cctcgagcgc gggcattctg tggtggcagg
     1321 ggcagcagat actcgagaac tacacgacca tccgggagca gaagaacacg caggccatgc
     1381 tgtcagagag gaacagcggt gtgcagctca cgacctgcgg agagcagaga cgccgctgcg
     1441 tgagggtgaa cccggaagcg ggacagttcg gagaggactc gagctggatg atactggcgg
     1501 ggaaatagca catgacggag ctggaaaaac agttgctgag cgcattagag cagctacagc
     1561 aggactactc gaaaaggctg gacgagtggg agaacgcctt cgcggaatgg cggacgatgt
     1621 ctggtcttat gcaacgggag aacgcggcgc tgagcgagcg cgtcacgggc ttgagcaggc
     1681 aggtgcagag tttgagcgag cagcttcgcc ggttgtcgtg agactagacg gcattgaagc
     1741 acaccgggag catgagcggg cggtgcagca ccagaaaacg ctggagcttg aacgatcgca
     1801 gcggcagcgg acgtacaatg gaccgtcgct gtaacaaacc ggataaaacg gggctttcgg
     1861 cgaatatctg cggcgaaagc cggtgccatt cacctgtctg catggctatg cattcgggtg
     1921 aaatttatca ggcgcaggcg gcgcgtttta ccggggagtt aactgtattt ttttccgggc
     1981 tgacggcgca ttcgcgctga acccgtccgg agcggtgccg gtaagagatg ttatggtaaa
     2041 tgattctgaa ttaaactaat tttcccttct ttcacctttc tgtgtaaaaa tatgtactca
     2101 atttatacac caactgataa actctattca aagcacggac actggccacc atgtgccata
     2161 gcgagaattt gtactggcct aataaatcaa cactgaaacc tgaaacctga aacctgaaac
     2221 cacaaaccgg aaactatgac ccttgaatcg tgcagcgccg ttctcgccgg aagcgcccct
     2281 atatgatgag aaaaaaatgc ctatgaacca gaccatgtcc cagaaactcg caagagacag
     2341 tctcggaaat gcacaaacct ttgaaggagg tgtttacgtc actaaaaacg gagtagctga
     2401 gttattcatc caaaccgcag cagaacgtga tgctgaagtt cgtgagatga gagaagaacg
     2461 caatatcaac gcccttttta agctggcaac gttggctaaa aaggaaatca cagaaggcaa
     2521 aggcatgacc ccagaagagg tcttagggag gttgcgtgcc gctagaaaat aacagagagg
     2581 tgtttagtgt cccagcaata cacggtttca atcgcgccga tggcatatca atgtttagct
     2641 gatatcgagt cttacaagag tggatacatt gggtcactca aggccggtga tctggttgat
     2701 aacttacttc aggaatcagt tgcctgcatt atccaagacc ctgaacgtta tcactacaat
     2761 ttccacttac aggatcgagg tatgctttta cgtgagcggc tcgatgttga gagtgaatac
     2821 agggtgcttt acgattttga cggaacgaac atcgaaatac tgttgtttgt gagcatgaag
     2881 caggattttt gaaaagcagc tgtatcgcta taatttgctg aattaacact aaacacccgg
     2941 catcgtcggg ttttttcgtg cagacaaaaa tttccaccta tgcctattaa cactaagtta
     3001 gtagatatag gtgggcttac gtgtccttat ttaaaacttt cgactttgac catgaactct
     3061 ttaatggaaa cgatcgctgt cgctttacct ccagggatgc tttgcgccga gaagtcgatg
     3121 tcttgatttc cttggcttgt gtgtatgcga atgcggcagt ttttagctga taccatgctc
     3181 tccagcaatt tataggggat aacaacagtg ttcttgctag aggtatagat cgttttagat
     3241 acggagttat atgcgctact gcttagatta gtttgctgct gtgctttata gctggatatt
     3301 ttgccatcaa tatttatatc aatccccgtc aaacctaagt atgcggcatt tccgctagat
     3361 acattcgagt tgtaggaaag aattagccca acctcttctg gataggcact agaccatatc
     3421 gcgcccaact gaagttgtgt tccccaagtg ctgttaggat cgtatagcga atttggagat
     3481 acctctataa cggtcgagtt atcaaaggtt gatgtttgct gagaaacaac acccattcct
     3541 gccaatttat ccattgctgt acagccagag atggctatta cgattgcaga agcaaaaaaa
     3601 atctttctta tcattttttt gacctttttg gtttgttttc cagagagtga aatagcattg
     3661 tatttctgaa actatcttga aggcttatag ctgttttaaa cagtgttttg aacacagagt
     3721 tgaaggatct tcttgagatt ctcgggtggg agtcgtaatc tcttgaccca gaaacgaaaa
     3781 aaccacctgg ggaggtggtt tttcgatggt tcagtaagtt ggggaacttc tgaaccgtgg
     3841 taacagggtg tacaagaccg ctgccaccaa attcgtcctt ccagtttagc cgtagttggg
     3901 ctgatacttc aagaactctg cgttagtaat ctcttgtaca tcctcttacc aatggctgct
     3961 gccagtggcg ataagtcgtg tctttccggg ttggactcaa gatgatagtt accggataag
     4021 gcgcagcggt cggactgaac ggggggttcg tgcatacagt ccagcttgga gcgaactgcc
     4081 tacccggaac tgagtgtcag gcgtggaatg agaaaccgcg gccataacag cggaatgaca
     4141 ccggtaaacc gaaaggcagg aacaggagag cgcatgaggg agctaccagg gggaaacgcc
     4201 tgggatcttt atagtcctgt cgggtttcgc cgccactgat ttgagcgtca gatttcgtga
     4261 tgctcgtcag gggggcggag cctatggaaa aacggcaacg ccgcatcctt tttctgttcc
     4321 tttctgatgt gtcgccttcc gctttatctc gttatccgtg agcctgtaac gcccgccgca
     4381 gtctcacggc aggagcgcag cgaccgagtg agcgaggagg cgtcatttca cttttaccta
     4441 cattctgcac ttacgcccca cagccgcatt tttcctctgt cacatgaagc acttccctga
     4501 attcccactt cgatttacta tattaagcca gtatacactc cgctagcgct acgtgactgg
     4561 ttcagggctg cgccccgaaa cccgctaaaa gccactgacg cgcctgcggc ttgcccaaca
     4621 ccgcgccgcc cgggaaagaa tttcccgccc gtcccggcgt tatcaggagg ccgga
//
