LOCUS       CP123690                6238 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg strain
            FSIS11813680 plasmid pFSIS11813680-2, complete sequence.
ACCESSION   CP123690
VERSION     CP123690.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN09954714
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Senftenberg
  ORGANISM  Salmonella enterica subsp. enterica serovar Senftenberg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6238)
  AUTHORS   Ge,B., Mukherjee,S., Li,C., Harrison,L.B., Hsu,C.H., Tran,T.T.,
            Whichard,J.M., Dessai,U., Singh,R., Gilbert,J.M., Strain,E.A.,
            McDermott,P.F. and Zhao,S.
  TITLE     Genomic analysis of azithromycin-resistant Salmonella from food
            animals at slaughter and processing, and retail meats, 2011-2021,
            United States
  JOURNAL   Microbiol Spectr 12 (1), e0348523 (2024)
   PUBMED   37991374
REFERENCE   2  (bases 1 to 6238)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (05-SEP-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 6238)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 257x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 10:46:17
            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)                     :: 4,755
            CDSs (total)                      :: 4,635
            Genes (coding)                    :: 4,519
            CDSs (with protein)               :: 4,519
            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)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 44 of 116
            Pseudo Genes (incomplete)         :: 83 of 116
            Pseudo Genes (internal stop)      :: 18 of 116
            Pseudo Genes (multiple problems)  :: 25 of 116
            Pseudo Genes (short protein)      :: 1 of 116
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..6238
                     /organism="Salmonella enterica subsp. enterica serovar
                     Senftenberg"
                     /mol_type="genomic DNA"
                     /strain="FSIS11813680"
                     /serovar="Senftenberg"
                     /isolation_source="animal-cattle-steer"
                     /sub_species="enterica"
                     /db_xref="taxon:28150"
                     /plasmid="pFSIS11813680-2"
                     /geo_loc_name="USA:KS"
                     /collection_date="2018"
                     /collected_by="USDA-FSIS"
     gene            complement(25..939)
                     /gene="lpxO"
                     /locus_tag="D3F45_23700"
     CDS             complement(25..939)
                     /gene="lpxO"
                     /locus_tag="D3F45_23700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001728425.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_process:
                     GO:0018193 - peptidyl-amino acid modification [Evidence
                     IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="lipid A hydroxylase LpxO"
                     /protein_id="WGN64995.1"
                     /translation="MLSLIIIFVFLISVLYAHSRGKIKQKFSRQLFDHSTFMAPINMFM
                     TGFSKLPSKQAWFPPETFPELQPLIDNWQVIRDEAVNLQGHIKSSEKNNDAGFNTFFKR
                     GWKRFYLKWYGDAHPSAERLCPVTTQLVSSIPCIKAAMFAELPSGSHLGKHRDPYAGSV
                     RYHLGLSTPNDERCFIEVDGVRRSWHDGEVIIFDETFVHWAQNDTEQTRIILFCDIERP
                     MKWRWSQKINRWIGGVLMSAAASPNDNNDRTGAINHLFKYVNAIRDAGQKLKKRNRKLY
                     YLIKNGVISLIFVWLAVSVFRWL"
                     /name="lpxO"
     gene            complement(1210..1425)
                     /locus_tag="D3F45_23705"
     CDS             complement(1210..1425)
                     /locus_tag="D3F45_23705"
                     /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="WGN64996.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSSG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1429..1914)
                     /locus_tag="D3F45_23710"
     CDS             complement(1429..1914)
                     /locus_tag="D3F45_23710"
                     /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="WGN64997.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSVLLIASNAAILWWQSQQIL
                     DNYVSIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(1949..2383)
                     /locus_tag="D3F45_23715"
                     /pseudo=""
     CDS             complement(1949..2383)
                     /locus_tag="D3F45_23715"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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(2592..2915)
                     /locus_tag="D3F45_23720"
     CDS             complement(2592..2915)
                     /locus_tag="D3F45_23720"
                     /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="WGN64998.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3559..3669
                     /locus_tag="D3F45_23725"
     CDS             3559..3669
                     /locus_tag="D3F45_23725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WGN64991.1"
                     /translation="MHDPPVQSDYHAHSGNYQLESNPERHDKIAIGGSHW"
                     /name="replication initiation protein"
     gene            complement(3924..4385)
                     /locus_tag="D3F45_23730"
     CDS             complement(3924..4385)
                     /locus_tag="D3F45_23730"
                     /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="WGN64992.1"
                     /translation="MVNTYYGYLLGVTLGEWAMGSDVQWQIDNGYLAQVMGDFSTESPS
                     FETPMFGRYFDTFQAAIHVAKAFPGSTLQPSEYEDKTGMLIRHYYVDCHPYYDRLPPEK
                     SDNFQYDEYPSAIHVAACIDQASKELDELLFGGGYGENGEGHASPIILY"
                     /name="hypothetical protein"
     gene            complement(4468..5058)
                     /locus_tag="D3F45_23735"
     CDS             complement(4468..5058)
                     /locus_tag="D3F45_23735"
                     /inference="COORDINATES: protein motif:HMM:NF019843.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0005515 - protein binding [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="tetratricopeptide repeat protein"
                     /protein_id="WGN64993.1"
                     /translation="MPSLSVERWLALATAGDSQARFHLGKIFSCGLGVHQDYKQAIYWF
                     QLAAEQGHDDAQFSLGWAYHLGLGGYKDAQKASEWYQKAAEQGHAEAQFQLGRLYAFSD
                     LRNDALAVEWFLCAAKQDHSSAQFKLGWMYHLGMGVEQSDRQAFHWFILAAEQDHAGAQ
                     ASLGEMYKNGWGVEQDDVAAQDWFYRARTMHYP"
                     /name="tetratricopeptide repeat protein"
     gene            complement(5063..5599)
                     /locus_tag="D3F45_23740"
     CDS             complement(5063..5599)
                     /locus_tag="D3F45_23740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005200081.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN64994.1"
                     /translation="MLDTDCITVLTARGITEILNSGGSQAWRLDATHVAKLPYLVCVQN
                     SKKDWGSQEAKHHHAFMIGKISGVSRAPENPKRWIINIDSYAEIDIPGQWDGNRNPVSY
                     RKLEDMGIDISKVDFQPLPKEDSLVLNTIKGGDEYDEYEEDSNRVRPINLKEAKAGLAL
                     YFGVNEDDIQITIKG"
                     /name="hypothetical protein"
     Typing          complement(3017..3203)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.911"
                     /coverage="87.0"
                     /evalue="2.69e-52"
     Typing          3183..3669
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.959"
                     /coverage="93.0"
                     /evalue="3.59e-159"
     Typing          complement(1113..2602)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatgactcaa tagaaaaaaa caaatcacag ccatctaaac actgagacag caagccaaac
       61 aaaaatcaaa gaaataactc catttttaat caaataatat agttttcgat tccttttttt
      121 tagcttctga cctgcatcac gaatagcatt aacatattta aataaatgat ttatagcacc
      181 agtcctgtca ttattatcgt tgggtgatgc tgccgctgac attagcaccc cacctatcca
      241 cctatttatt ttttgtgacc accgccactt catcggcctt tctatatcac agaacaaaat
      301 aatacgtgtc tgctcggtat cattctgagc ccagtgaaca aaagtttcgt caaaaattat
      361 cacttcacca tcatgccaac tgcggcgtac accatcaact tcaataaaac accgttcatc
      421 atttggtgtt gataatccta aatgataacg aactgaaccg gcataagggt cacgatgctt
      481 tcctaaatgg cttcctgaag gcaattcagc aaacatcgct gctttaatac agggaataga
      541 gctaaccagt tgggttgtta ctgggcaaag ccgctccgct gatggatgag catctccata
      601 ccacttgagg taaaagcgct tccaaccgcg cttaaaaaat gtattaaatc ctgcatcatt
      661 atttttttca gatgatttaa tgtgcccttg caaattaaca gcttcgtctc ttataacctg
      721 ccagttatca attaatggtt gaagttcagg aaatgtttct gggggaaacc atgcctgctt
      781 tgacggcagc ttcgaaaagc ctgtcataaa catatttatc ggagccataa atgttgaatg
      841 atcaaataac tgcctggaaa acttttgttt tattttaccg cgagaatgcg catacaatac
      901 actgataaga aaaacaaaaa taataataag tgacagcatg tgtatattcc ttgttcacgc
      961 caataataaa aatctcttaa agataacata atgaatgcac ttaaattata atctaaatgc
     1021 tatttatcaa tagtataatc gaagcttcac cagaacatat ctactacaca ggcagagagg
     1081 atttcagcag gaattatgct gaaatgaatc aaagggacgg accgtgatat acccgctgtc
     1141 gctgtgatcg ttccagctcc agcgctttct gatgccgcgc ctcccgcacc tgctgcagct
     1201 cgacggcatt cagccgctcg acaaccggcg cagctgatcg ctcaaactct gcacctgcct
     1261 gctcaagccc gtgacgcgct cgctcagcgc cgcgttctcc cgttgcataa gaccagacat
     1321 cgtccgccat tccgcgaagg cgctctccca ctcgtccagc cttttcgagt agtcctgctg
     1381 tagctgctct aatgcgctca gcaactgttt ttccagctct gtcatgtgct atttccccgc
     1441 cagtatcatc cagctcgaat cctctccgaa ccgtcccgct tccgggttca ccctcacgca
     1501 gcggcgtctc tgctcgccgc aggtcgagag ctgcacgccg ctgttccgct cggacagcat
     1561 cgcctgcgtg ctcttctgct cccggatgct cacgtaattg tcgagtatct gctgactctg
     1621 ccaccacaga atggccgcgt tcgaggcgat cagcagcacg gagaccagga cgatggtcag
     1681 ccacgtctgg ctgaccatgc gcagcatccc tttcgtacgc tggctcatgg ctgaggacag
     1741 cttccggtcg tggtcgagga tggcggcgct gattctcttc tcgctttcgc tcagttccgc
     1801 tctgacagac ttctcgtgct cgctgaatgc ggctttcagc atctcgccgg tactctgctg
     1861 ctgcgctttc gatttctgct ctaagtcctt cgccagcgtt aaaagactgt tcatagatgg
     1921 ctcccttcag tcggatgttt cgccccccgt ccgggtcggc aatgctgatg ctgctttttg
     1981 tggtgcgtac cacctcaaaa cctgcgcttt ccagcgcctc agtgacgtcc tggcgggttt
     2041 tcagctcccc ggacgaggcc aaggccagta aaccccgtgt aattgcctga gcggcttcct
     2101 gcttcgtttc cggcagcgcg gacggcgtga ccagcgcccg ccggttttca ggcgcgttcg
     2161 ggtcatgcag ccccagcctg ccgttcacga tggtctgcca ggcatcaatg cgcggacggt
     2221 cggcgcggtc atagtatggc tggagccgtt tgccggtcag cagctccgtg ttcgggatca
     2281 ggaagttcag ctccagccgc cccttatcct ggtgctcaac ccacagcacg ctgtactggt
     2341 ctttgtcgag tccgggcatc agaacccgtt caaagctcgc catcagcttt tcgcgctgcc
     2401 cgggcggtaa atccttttcg gcaaaggaca ggacgccgga tgtgtacttt tttgcgtagg
     2461 gtgaggcgtc gataagctcc ctgacttctt ccggcttccc ctgcagaacg gtggcgccct
     2521 cgcgctgtcg gtctttcccc agcagataat ccaccggacc ggcgccaccg ccgcgccctc
     2581 gcgggtgaaa cttaacgatc atcgtctgca cccttttcca gcacggcatg ccgcagccgc
     2641 tcgagtccgg catctatggc catcagcgcg gcgacgacct gcacgcggtc gtgcccgctg
     2701 ccaccaccgg cgttaacctg ccgggcaatc tggttaaggt tgttccccat gccggcaagc
     2761 tgacgaagca gcgccggcga gatcgaggga agcttgccgg cgcgggcggg tttctcgtcc
     2821 aggcacgtct ggcgcatcca ggctgcaagc tgtttaccgt cgcagcgctc cagcagacgc
     2881 cggtgctcat cctcggtcac ccacatcgtg agcattttgc tgcgtttgtc tgccaatccg
     2941 gcctcctgat aacgccggga cgggcgggaa atcttttccc ggtcggcgcg gtgttggaca
     3001 agccgcaggc gcgtcagtgg ttttagcggg tttcggggcg cagccctgaa ccagtcacgt
     3061 agcgctagcg gagtgtatac tggcttaata tggtaaatcg aagtgggagt tcagggaagt
     3121 gcttcatgtg gcaggtaaaa aatgcggctg tggggcgtaa gtgcgaaatg ctggggacga
     3181 tgaaatgacg cctcctcgct cactcggtcg ctacgctcct gccgtgagac tgcggcgggc
     3241 gttaccggct cacgaatggc gggataaaga gatggcgctc aaatcaggaa gggctgggaa
     3301 aaggatgcgg cgttgccgtt tttccatagg ctccgccccc ctgacaagca tcacgaaata
     3361 tgacgctcaa atcagtggcg gcgaaacccg acaggactat aaagatccca ggcgtttccc
     3421 cctggtagct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg
     3481 ctgttatgtg gccgcgtttg tctcattcca cgcctgacac tcagttccgg gtaggcagtt
     3541 cgctccaagc tggactgtat gcacgacccc cccgttcagt ccgactacca cgcccattcc
     3601 ggtaactatc aacttgagtc caacccggaa agacacgaca aaatcgccat tggcggtagc
     3661 cactggtaag caggatgtgc gagagatgta tcgagagttc ttgaagtggt ggccggacta
     3721 cggctacact ggaaggacag atttggtgac acgtctcgca caagactgtt accacggttc
     3781 agaagttccc caacttactg aaccttcgaa aaaccacctc cccaggtggt tttttcgttt
     3841 tcagagcaag agattacgcg cagagcaaaa cgatctcaag aagatcattt tacaaattgg
     3901 ataatatccc tccgccccta acactaatat aaaattatcg ggcttgcatg cccctcacca
     3961 ttttccccat atccaccacc aaacaatagt tcgtcgagtt ctttgctagc ttgatcaata
     4021 cacgcagcca catgaatagc agaagggtac tcatcatact gaaaattatc gcttttttca
     4081 ggagggagtc gatcataata cggatgacaa tccacataat aatgacgtat tagcatccca
     4141 gttttatctt cgtactctga tggctgcaac gtactccctg ggaaagcttt tgcaacatgt
     4201 atagcagctt gaaaggtatc aaaatatcgc ccaaacattg gcgtttcaaa gctaggcgac
     4261 tctgtcgaaa aatcccccat aacttgcgcc aaataaccat tatctatctg ccattgaaca
     4321 tctgatccca tagcccactc tcccagagtt actcctaata aataaccata atatgtattt
     4381 accataacgc ttcatgttat gaatcagcag cagccagctc cgcaagcctc ttacacgtag
     4441 gcgtaaaaaa acccgcacag ggcgggttta gggatagtgc atggttctgg cacgataaaa
     4501 ccaatcctgc gcagcaacat catcttgctc gaccccccat ccatttttat acatctcacc
     4561 aagagatgcc tgagctcctg catgatcttg ctcagcggcc agaataaacc aatggaaagc
     4621 ctgcctatca ctttgctcaa cgcccatacc gagatggtac atccagccaa gtttaaattg
     4681 ggcactactg tggtcttgct tcgcagcaca gagaaaccat tcgactgcta acgcatcatt
     4741 tcttaaatca gagaaagcat acagccttcc aagctgaaac tgagcctctg catgaccttg
     4801 ctcagcagct ttctgatacc attccgaagc tttttgagca tctttatatc cacctaaccc
     4861 cagatgatat gcccaaccaa gactaaactg ggcatcatca tggccttgct cagctgcaag
     4921 ctgaaaccag tatatagcct gcttataatc ctgatgcaca ccaagaccgc atgagaatat
     4981 cttacccaga tgaaatctag cctggctatc tccagcagta gctagtgcta accagcgctc
     5041 aacagagagt gacggcataa ggtcatccct taattgtgat ctgaatatca tcctcattca
     5101 caccaaaata taaagccaac cctgctttag cctcttttag atttatcggc ctaactctgt
     5161 tgctatcctc ctcatactca tcatattcat ccccgccttt tatcgtattc aagactaagg
     5221 aatcctcttt aggtaggggt tggaaatcca ctttggagat atcaattccc atgtcttcaa
     5281 gttttctata ggagactgga ttacgattgc cgtcccactg cccagggata tcaatttcag
     5341 cataggaatc aatatttatg atccagcgct tagggttttc aggggctcga cttactccgg
     5401 atattttccc gatcataaat gcatgatgat gcttagcctc ctgactaccc cagtcttttt
     5461 tcgaattttg gacgcaaacc aggtacggaa gcttagctac gtgagtagca tcaagtctcc
     5521 aagcctggct tcctccacta tttaaaatct cagtaatacc cctggccgta agaacagtaa
     5581 tgcagtcagt atcaagcata gatatctcca tttttgtttt aaaaaaggca agtcaccgcg
     5641 taatgacaat ctttttagca tcaaaaacgg aagagctcaa cataaaacca caagatatat
     5701 acaaataact atccgaagta ctacgacgat tacccctagg gctgcaaaaa aatcagtaaa
     5761 acactactcg acttcggccg gagggctttt tctctctgga ctcagtctga gtgacaacat
     5821 gatgtgtgaa gtaagaaccc gccacaccgc cgcatttaac ataagagttc tttggccgca
     5881 ccccctgaga gcccctcagc gcgtttctgc ggcctgaggg ccgtttccgg cacctttccc
     5941 cggcccaaac cctgaaaaac gcccctgata atttctgcgc ggctgcatgg ctatgcacaa
     6001 gagtgaatgg cggccggttt cgtgaaggaa ataccgtgaa agctccgaaa gaaacgctta
     6061 attgcacagc agcacatgaa cgtgatcaga tgaaatctgt ctactgccgc acttcttcac
     6121 gaaaggcccg ctgagcgtca gattcgggcc tttcttacta aaaagatttc aatagaattt
     6181 tttagcaggc gatttttatc tataaccata cattgagcat agaagaccca aatttatg
//
