LOCUS       CP123695                4165 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11809860 plasmid pFSIS11809860-3, complete sequence.
ACCESSION   CP123695
VERSION     CP123695.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN09372566
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4165)
  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 4165)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4165)
  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                   :: 294x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 11:07:37
            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)                     :: 5,220
            CDSs (total)                      :: 5,094
            Genes (coding)                    :: 4,973
            CDSs (with protein)               :: 4,973
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 35 of 121
            Pseudo Genes (incomplete)         :: 95 of 121
            Pseudo Genes (internal stop)      :: 18 of 121
            Pseudo Genes (multiple problems)  :: 26 of 121
            Pseudo Genes (short protein)      :: 1 of 121
            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..4165
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS11809860"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pFSIS11809860-3"
                     /geo_loc_name="USA:VA"
                     /collection_date="2018"
                     /collected_by="USDA-FSIS"
     gene            complement(33..227)
                     /locus_tag="DNB19_26045"
     CDS             complement(33..227)
                     /locus_tag="DNB19_26045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="WGN69969.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1316..1726
                     /locus_tag="DNB19_26050"
     CDS             1316..1726
                     /locus_tag="DNB19_26050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN69970.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            1984..2547
                     /locus_tag="DNB19_26055"
     CDS             1984..2547
                     /locus_tag="DNB19_26055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN69971.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(2576..3202)
                     /locus_tag="DNB19_26060"
     CDS             complement(2576..3202)
                     /locus_tag="DNB19_26060"
                     /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="WGN69968.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHINDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     Typing          264..367
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.286"
                     /coverage="100.0"
                     /evalue="4.87e-36"
     Typing          492..747
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="89.0"
                     /evalue="1.25e-96"
     Typing          complement(3479..3992)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgggaaagcc gtgaccgcct ccgtcagctt cgttatgttc ctgtttcact ttcggcctca
       61 aagcgaatct ggatgctgtt ctggagttct tctgcgagtt cgtgcagtcg ttcgcacatg
      121 gccgcctgtt cgtcggcatc cagagcatcc agtttttcaa gcagtgtcag gctctggctt
      181 ttgataaatc gcgccatatt cagcgcagtt tgttgttgtt tgttcacctt ccgttgttct
      241 ccgtcagttc cgggtgtcgg ggggaccctg agcaggtggt aattgtaaga cgttgcgggc
      301 gacggtatta caattgcaca tcctgtcctg tcctgtttct ttaggacgta tcatggcaca
      361 gcatatcaac tgataaataa tccctgtgca gtgcagccgc tgttgcataa aatttcgctc
      421 tgcgtcgagt gtttcttaat caataattcc gctgatactc cggaaaaacg cgagtctgtt
      481 ctcatgcctg aaatgcccac accccacgca aaaacaagtt tttgctgatt tttctttata
      541 aatagagagt tatgacaaat tagttcttct tgctctcttt gtgatattta aaaaagcggt
      601 gttggcgcag ctacaacacc gcgccgacac cgctttttag gggtggtact gactattttc
      661 ataaaaaaca tcatcttata ttaggggtgc tgctagcggc gcggtgtgtt tttttacagg
      721 acgcccctgg gggcgctgcc aggggtgtct gttcagatat gtagcaatga gtcagggatt
      781 cacgaactga aaatgtccga aaatgtgtct catgggtact gtatgcgccc aaaccgatcg
      841 tcattcactt tcatgcatag ctatgcagtg agctgaaagc gatcctgacg catttttccg
      901 gtttaccccg gggaaaacat ctctttttgc ggtgtttgcg gcagaatcgc gttcagcgcg
      961 ttttagcggt gcgcgcaaga actcttatgt taaattcatc tcatcggcaa cctatacagg
     1021 cataaaaatc agtttctata agcggctttc ttgcacctac ttggtgattt ttttggatgc
     1081 gctgacgttg ctcgacttta aatcaccata gaaaaatacc ctttacttac ataaagatcg
     1141 atctggatgt gtatcttgac gaggttcaat acgagcaatt gtttttgtat ttaaggtttc
     1201 ttatcgccgt tttttgcggc tctagaaaaa tcaatacaaa agatcttgaa agtcacctcg
     1261 ctccctgggt acactttcgt ataagaactg atcgatgtct aaaacggatt gtattatggc
     1321 ctttatctct ctatcgaact tggcagcgaa gactggaagg ataatccagt cgcagtgtgt
     1381 tacggccacg caaacgaaaa aaagcacggg cgctgtcgag ctgggattcc gcttgagcaa
     1441 gagcgctatg gacgagactg gtattaccat tggggatcgt gtcgacattc tttacgacaa
     1501 agaagaaaac cagtggatga ttaagaaaat tagtgaaggt ggctttggtg tgtctgggca
     1561 aaaaaacaag cacggcggtt actcatcgtg tgctgttaga ttgaccttgc gaccaggttt
     1621 tcctcgcctt tctgaggatg aagaggacaa caagaagcta ctttccgatg attcattcac
     1681 tcagctaagt gaaggtgtaa tcgtcttcag gctggatgat gaataggaag gaccaaaaag
     1741 gaaaggcaga gttagtgagc gtcgccaaac aatcgactaa ctccgccttc tggtcaacac
     1801 atcactacct ttggaagggt ggagtgttat gggcggcatt atgttcataa acttgcattc
     1861 taataaagaa aaaatcgttt cttttgaggg atgtgaacac gacattttct attctgatag
     1921 gtgcgatgct attggctttg gtctcttaag tttatgtttt taaaaacata tgaggctata
     1981 catatgcacg ctttatcaat actaccttca gttgcccgcg ctaacctggc aactaaattc
     2041 tcgtctcatt tgaaggtgat cgagctcttc aacacgatgc aggattccca agttgttgtc
     2101 ttgtcatcac tgatcgaagg ccatcacctc accagttctg gtaacagtgt caaagccgac
     2161 tttgaggtca ctcgcttacc ggcgattatc gagatgttag agaaaaaata ttttttccct
     2221 attcgtcatc taaatgtatc tgttaaatct gtaactacag gaaggatgac tggacaaact
     2281 gtctatttca tagagcctga acacatcgag caacttctcg ctgatcctga gcttgtgttt
     2341 gctaatcagg aaaggagcct cttctttcgt tctctcgaaa aagaagggaa aaatctcggc
     2401 aagcttatcg agaaaaaagg tagtgtttct caagccgtct taagccttct acatcacgcc
     2461 tacaaagata aacctctttc tgacgagatg tggaaggaga tagaagataa gttcacccat
     2521 atgctggatg aattgagcgc ggcgtaaagg caagggcggt cgttagaccg cctttttagt
     2581 cttctaaacc taattctttg tgatagtttt tcagcgtaga gtaacgatag tttctgagta
     2641 tgttttcatc tttcttgacg ttcgcttcta tgtatctgtt tacgaatttg ttgaaatctt
     2701 cttgtatttt ttctttgtta tcattgatat gggtaaattc aggagttggt atcttatagg
     2761 ctcgcgatac atactcttct ttcttaatta gcaacgcttt ggtgtaatcc agtcctttct
     2821 taacaccttc tgatcgctcc gaaacgaatc caaatttatg gtttaaatgg cttcgtaagg
     2881 gtatcccgaa caccaatccg ttgagatcaa taactacgat tccgtagcct cttacttttc
     2941 catcattact gccgtcgaga gcctcttgta ggcctttgtt atcagcataa aactggtctg
     3001 taagggttct taactgtatg taatcctgtt tgctcatttt tgatgtccat tggcattttc
     3061 ctgtaaccaa tgtacaaaaa aagcaaagcc ctctgtaaga gagggctttg cttttctttc
     3121 gttgagtctt ggatttttta cgtgtggcga actctaccgc acatctttct ttggaagctt
     3181 gtttgtttaa cgtggggctc attcctaccg ccacttctag atttacttat atcaaaaatt
     3241 atatgtgaag tcaatttcgt agctgttctt gactggactt actttgccag cgtaatcttc
     3301 tcctgaaacg aaaaaaccac cctggcaggt ggtttttcga aggttattta atcctggcag
     3361 attatctaac cgtggtaaca gtcttgtgcg agacgtgtca ccaaattcgt ccttccagtg
     3421 tagcctcagt aaggccacca cttcaagaac tctcaataca tctctcgcac atcatgttta
     3481 ccagtggccg ttgccaatgg cgattagtcg tgtctttccg ggttggactc aagtcgatag
     3541 ttaccggaaa aggcgcagcg gtcggactga acggggggtt cgtgcataca gtccagcttg
     3601 gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagataaac gcggccataa
     3661 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagccacc
     3721 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccaccact gatttgagcg
     3781 tcagatttcg tgatgcttgt caggggggcg gagcctatgg aaaaacggca gcgccgcatc
     3841 cttttcttgc cctgtttgtc atgccgtatg cctttgctct tatccgtgtg caggtaacgc
     3901 ccgccgcagc cgaacggcag gagcggaagc gaccgagtga gcgaggaggc gtaatgtcac
     3961 cgcaacctcc atgttctccc gtacgccctg cagctgcatt ttcccctgcc acatgaagca
     4021 cttttataaa gtgttactcc gccgtaacat attaagccag tatacactcc gctatcgcta
     4081 cgtgactggg tcatggctgc gccccgacac ccgctaaaac cccctgacgc gccctgacgg
     4141 gcttgtctgc tgacgaaaac gccca
//
