LOCUS       NZ_CP028175             5572 bp    DNA     circular CON 01-DEC-2023
DEFINITION  Salmonella enterica strain CFSAN064033 plasmid pGMI17-001_3,
            complete sequence.
ACCESSION   NZ_CP028175
VERSION     NZ_CP028175.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08663434
            Assembly: GCF_003030125.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5572)
  AUTHORS   Hoffmann,M., Pedersen,S.K., Sanchez,M., Pettengill,J.B. and
            Hendriksen,R.S.
  TITLE     Genome assemblies for Global Microbial Identifier (GMI) Proficiency
            Testing reference strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5572)
  AUTHORS   Hoffmann,M., Pedersen,S.K., Sanchez,M., Pettengill,J.B. and
            Hendriksen,R.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAR-2018) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 425.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/01/2023 04:02:51
            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)                     :: 4,578
            CDSs (total)                      :: 4,456
            Genes (coding)                    :: 4,335
            CDSs (with protein)               :: 4,335
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 61 of 121
            Pseudo Genes (incomplete)         :: 75 of 121
            Pseudo Genes (internal stop)      :: 15 of 121
            Pseudo Genes (multiple problems)  :: 26 of 121
            Pseudo Genes (short protein)      :: 1 of 121
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP028175.1.
            Bacteria and source DNA available from Bacterial culture available
            from Dwayne Roberson, FDA College Park Campus, 5001 Campus Drive,
            College Park, MD 20740.
            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/
            There are 2 base modification files available for this genome.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5572
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="CFSAN064033"
                     /isolation_source="turkey"
                     /db_xref="taxon:28901"
                     /plasmid="pGMI17-001_3"
                     /geo_loc_name="Germany"
                     /collection_date="2009"
                     /collected_by="GMI"
     gene            36..226
                     /locus_tag="C6649_RS24120"
                     /old_locus_tag="C6649_24085"
                     /pseudo=""
     CDS             36..226
                     /locus_tag="C6649_RS24120"
                     /old_locus_tag="C6649_24085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1371..2237)
                     /locus_tag="C6649_RS24140"
                     /old_locus_tag="C6649_24105"
     CDS             complement(1371..2237)
                     /locus_tag="C6649_RS24140"
                     /old_locus_tag="C6649_24105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(2239..3291)
                     /locus_tag="C6649_RS24145"
                     /old_locus_tag="C6649_24110"
     CDS             complement(2239..3291)
                     /locus_tag="C6649_RS24145"
                     /old_locus_tag="C6649_24110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(3772..4005)
                     /locus_tag="C6649_RS24250"
     CDS             complement(3772..4005)
                     /locus_tag="C6649_RS24250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4012..4542)
                     /locus_tag="C6649_RS24255"
     CDS             complement(4012..4542)
                     /locus_tag="C6649_RS24255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4580..5278)
                     /locus_tag="C6649_RS24580"
                     /pseudo=""
     CDS             complement(<4580..5278)
                     /locus_tag="C6649_RS24580"
                     /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            complement(5220..5543)
                     /locus_tag="C6649_RS24165"
                     /old_locus_tag="C6649_24130"
     CDS             complement(5220..5543)
                     /locus_tag="C6649_RS24165"
                     /old_locus_tag="C6649_24130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(305..389)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          413..955
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.708"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3669..5230)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 catgaacaga aatcccccct tacacggagg catcagtgac taaacaggaa aaaaccgccc
       61 ttaacatggc ccgctttata agaagccaga cattaacgct gctggagaag ctcaacgaac
      121 tggacgcaga tgaacaggcc gatatttgtg aatcacttca cgaccacgcc gatgagcttt
      181 accgcagctg cctcgcacgc ttcggggtga cggtgaaaac ctctgacaca tacagctccc
      241 ggagacggtc acagcttgtc tgtgagcgga tgccgggagc agacaagccc gtcagggcgc
      301 gtcagggggt ttcggggcga agccctgaac cagtcacgta gcgatagcgg agtgtatact
      361 ggcttaacca tgcggcatca gtgcagattg tatgaaaagt gcgccatgcc gggtgtgaaa
      421 tgccgcacag atgcgtaagg agaaaatgca gcttccgacg ctcttccgct tcctcgctca
      481 ctgactcgct acgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg
      541 taatacggtt atccacagaa tcaggggata acgccggaaa gaacatgtgc gcaaaaggca
      601 aagccggaga aaggccacgc cgatggcgtt tttccatagg ctccgccccc ctgacgagca
      661 tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca
      721 ggcgtttccc ctggaagctc cctcgtgcgc tctcctgttt cgaccctgcc gcttaccgga
      781 tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg
      841 tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt
      901 cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac
      961 gacaaagcgc cactggcagc agccactggt aactggacaa tgtgcgagat atttagagag
     1021 tacttgaagt ggctgccgga gtgcggctac actagaagaa caattttggt gactcgtctc
     1081 gcataagaca gttacctggt taagcagtct gcaagctgac ttaaccttcg atcaaaccgc
     1141 cctgcaaggc ggttttttcg tttacaggca gcagattacg cgcagaaaaa aaggatctca
     1201 agaggatcct ttgatctttt tgttacaaac gtctctattt gactcccctg agagcgtttt
     1261 agcgcgcctc tgaccccctt ggttacattc cgacaccaga aacgctcccg ttttttacgt
     1321 gcatttggca cggtatcgat ggaggccggg gggcaatcct gaacagaatg ttactcctct
     1381 gagtattttc tgttaagaaa atatacactt agcacagtta caataaatcc taccccctgt
     1441 aagaatgtga attgttcatc caaaaacaac catgacaaaa ataatgcaac tagcggaata
     1501 aagtacaaca ttatccctgc caaatgaact gggagccaac gcaaggagtt caagtaaaaa
     1561 caaaaagcta aaaaatattg taatattcca gatgaaaaaa caataatcac ggattccaac
     1621 ggaagataaa ttgatgattt agatataaaa ataaagagcg atgacagtat aagggagaat
     1681 gtcaactgtc cgctcaataa tgtgataggc tcaaacgatt taataaggcg agacgatata
     1741 acaacataaa atgctgccga taacacaccg gcaacaacaa gacaatatcc aacaatatta
     1801 ttcgatccat tactgatgtc tggcaaggct accaaaatac tgccaacaat tgcacctata
     1861 aggaacaata taaaatattg cggggaatta attttaactg agcaaataag aacagacaac
     1921 accaatataa acactgattc aagtgaaaaa ataattgatg cgcttcctgc tgaaataaaa
     1981 taaagtccgt agagtgtaaa agtatacgct aagaatggtt caaaaacgcc tgtcgcataa
     2041 gcaagtatcg cttttgagtt taatgggagt ttttttcttt ttataaaaag aactatccaa
     2101 gatagtatta ctgcactaca aatctgccag aaaaacaccc ctccggcatc tagttcttca
     2161 actccttttt tgctcattac gatagctgcc ccccatgaga acgctgctaa aaaagcaaaa
     2221 agcattcctt taatcatatt aatcatcctc tttctcataa aggggtttgt tttcaaattt
     2281 ccttggttga aaggagttaa aaaacataga tgcatcatct acaggaatac caataaactc
     2341 tccataataa ggatcatcta taggaaactc ttctaatgaa acataaaaca atacattcca
     2401 gttgaagatc attggatcac tattttctat ttcatggagc aatctttcat ccttagttaa
     2461 ttctcctgga attaatacat cagtatgata aaaaccgctg taataagaac tattaccggt
     2521 gtgcactggg catccaaaac gatccaaatt agattctgaa tgccatgttg tagaaatccc
     2581 ttccggatgt gaatacccac ccttaccaac agactgaata gtcatgttac gaatatccgc
     2641 taacgcttgt tcttgatctt tatagaaacc tttttctatc gccagcctca taaaatgccc
     2701 cggggcattt acagaaataa gtattccccc tggtattctt ctatcatgat ttcttgttct
     2761 atgagcagaa gagtaaaaaa cattaacacc agccttatat atttttagcc catctttatc
     2821 ctgaaatggt acgctttcag tataaataac atcctctttt attggatagc actctggcat
     2881 atgcagcgaa caaatatatt tttgtatgtc cactaactct tctgatggac gagcaaaggc
     2941 aagttgtgga tgaataaaat aaatgagatg cgcactgacc tctcctcttc ttgcgcgttc
     3001 tttaaaacga actctttcat tacgcaaaaa atcaaacaaa tgaccatcat cattatatag
     3061 ttgggggcta tttacaatag ataaatggaa atcaagccct ttaattttct tgcttgccaa
     3121 tttaccaaat acacagggct gattgcctga cacccatttt cttagtaaat cttcaatttt
     3181 atctttagaa gtttcgttaa agataaatga atgaatatta tcaatatctt ttccaaatga
     3241 aaaactggat gataattgtg gtagtttatt tatacgttgt tgaagattca tgaaagctcc
     3301 cacaagacac ctcatatatt tttttatata ctgaaactac attatattta ttaccggcgt
     3361 aaaacgaaat aatttattat cgttaccgat attttaaaaa aatcattatt tgcacagtgt
     3421 tcgagttgtt agtatcactc cttcctgaaa atccgctcca tttaccataa cgtcgcattg
     3481 tacgcaccgc caaaacgcgt tcggtgcgat cacggcagca gacaggtaaa aatggcaaca
     3541 aaccacccga aaaactgccg cgatcgcacc tgataaattt taaccgcatg aatacctatg
     3601 caaccagatg ctacaggcca cattagcccg ccttaatcca ctgaacacgt catttttcat
     3661 ggtttcacca tcccagcgaa gggccatcca gtgtccgctc ctggatttcc ggctgacgct
     3721 cccgctccag agataactca tgttcgcgtt cctgcatcag ccgttcatcc cttatctcct
     3781 gttctcgctg tataactggc tcaagcgttc tgtccgctcg ctcaagtgct gcacctgctg
     3841 actcaactgc atgactcgcc cgttcagcat cgcgttgtcc cgttgcgtaa gcgaaaacat
     3901 tttctgcaat tccacgaagg cgttctccca ttcgttcagc cgctgcatat agtcctgttg
     3961 cagttgctct aatgcgttca gcaaatgtct ttccagctcc gtcatgctct gtcactcctg
     4021 caccagtctc actgcgttca gtttgccgtt gtccttcgtc cagttcgttt cggctttcat
     4081 ccccttcggc aacaccagaa aacgtccgtt gctgtcctcg tgataacgca cgccccatgt
     4141 cttcgcgttc agcttctcca gactctcttt ctgctcgcgg agaatattca tattcgcgtt
     4201 tatcttcatg ccctggtacc acagcagact cccggtcgtg gcaaacatca gtactgagac
     4261 gataatcagc cacagccagc gtttcacgct cattttcagt acggttttcc agtgcgcgtc
     4321 catcgtatcg acggtcgttt tctgatacct ctccagcagt tctttcaggg ctgttgtatg
     4381 gtcgttgata gcgttcctga ttaaagattc gtttgaggtc agttccctgt ttacagattc
     4441 ttcgagcttc ctgaactcgt cgttcagcat tttctctgta gattcggctc tctctttcag
     4501 ctttttctcg aactccgcgc ccgtctgtaa aagattgctc ataaaacgct cctttcagtc
     4561 tgatattcct cccgccgttc gggtctgcaa tgctgatact gcttcgcgtc accctgacca
     4621 cttcaagccc cgcctctgtg agcgcctgaa tcacatcctg acggcctttt atctctccgg
     4681 catggtaaag cgcgtctatc ccgcgtgtga cgccctcagc aagcgcctgt ttcgtttccg
     4741 gcaggttatc aggaagggtc agcgtccggc ggttctccgg ggcgttgggg tcatgcagac
     4801 cgtaatggtg attcaccagc gtctgccagg catcaattct cggcctgtct gcccggtcgt
     4861 agtacggctg gaggcgtttt ccggtctgta gctccatgtt cggaatgaca aaattcagct
     4921 caagccgtcc cttgtcctgg tgctccaccc acaggatgct gtactgattt ttctcgagac
     4981 cgggcatcag tacacgctca aagctcgcca tcactttttc acgccctcca ggcggcagct
     5041 ccttctccgc gaacgacaga acacctgacg tgtatttctt cgcaaatggc gtggcatcga
     5101 tgagttcccg gacctcttcc ggattcccct gaagcaccgt tgccccttcc cggttacgct
     5161 cccttcccag caggtaatca accggaccac tgccaccacc ttttcccctg gcatgaaact
     5221 taactatcat cccgcgcccc ctgttccctg accgccagac gcagccggcg cagctcatcc
     5281 ccgatggcca tcagtgcggc caccacctga acccggtcac cggaagacca ctgcccgctg
     5341 ttcaccttcc tcgctgtctg gttaaggtta ttcccgatgg cggccagctg acgcagtaac
     5401 ggcggtgcca gtgtcggcag cttcccggaa cgggcaaccg gctcacccag gcagacccgc
     5461 cgcatccata ccgccagttg tttaccctca cagcgttcca gtaaccgggc atgttcatca
     5521 tcagtaaccc gtatcgtgag catcctctcg cgtttcatcg gtatcattac cc
//
