LOCUS       NZ_CP130128             4054 bp    DNA     circular CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SECVM-5 plasmid Col(pHAD28), complete sequence.
ACCESSION   NZ_CP130128
VERSION     NZ_CP130128.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361192
            Assembly: GCF_030505995.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Schwarzengrund
  ORGANISM  Salmonella enterica subsp. enterica serovar Schwarzengrund
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4054)
  AUTHORS   Sopovski,D., Commichaux,S., Zhao,S., Grim,C.J., Foley,S.L. and
            Khajanchi,B.K.
  TITLE     Complete genome sequences of 17 Salmonella enterica serovar
            Schwarzengrund strains carrying IncFIB-IncFIC (IncFII) fusion
            plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4054)
  AUTHORS   Sopovski,D., Commichaux,S., Zhao,S., Grim,C.J., Foley,S.L. and
            Khajanchi,B.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2023) Office of Applied Research and Safety
            Assessment, CFSAN, U.S. Food and Drug Administration, 8301 Muirkirk
            Rd MOD1, Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Hybrid assembly using Unicyler v. unspecified
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 37.1x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 12:14:50
            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)                     :: 4,977
            CDSs (total)                      :: 4,855
            Genes (coding)                    :: 4,685
            CDSs (with protein)               :: 4,685
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 77 of 170
            Pseudo Genes (incomplete)         :: 118 of 170
            Pseudo Genes (internal stop)      :: 30 of 170
            Pseudo Genes (multiple problems)  :: 49 of 170
            Pseudo Genes (short protein)      :: 1 of 170
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130128.1.
            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..4054
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="SECVM-5"
                     /serovar="Schwarzengrund"
                     /isolation_source="Chicken Wings"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="Col(pHAD28)"
                     /geo_loc_name="USA"
                     /lat_lon="37.0902 N 95.7129 W"
                     /collection_date="2013"
                     /collected_by="FDA"
     gene            join(3219..4054,1..304)
                     /locus_tag="QPE06_RS24855"
                     /old_locus_tag="QPE06_24855"
     CDS             join(3219..4054,1..304)
                     /locus_tag="QPE06_RS24855"
                     /old_locus_tag="QPE06_24855"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000900598.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_005761319.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            309..512
                     /locus_tag="QPE06_RS24860"
                     /old_locus_tag="QPE06_24860"
     CDS             309..512
                     /locus_tag="QPE06_RS24860"
                     /old_locus_tag="QPE06_24860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(1355..1549)
                     /locus_tag="QPE06_RS24865"
                     /old_locus_tag="QPE06_24865"
     CDS             complement(1355..1549)
                     /locus_tag="QPE06_RS24865"
                     /old_locus_tag="QPE06_24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="WP_052940196.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLALLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1832..2155
                     /gene="mobA"
                     /locus_tag="QPE06_RS24870"
                     /old_locus_tag="QPE06_24870"
     CDS             1832..2155
                     /gene="mobA"
                     /locus_tag="QPE06_RS24870"
                     /old_locus_tag="QPE06_24870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_001699352.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2379..2645
                     /locus_tag="QPE06_RS24875"
                     /old_locus_tag="QPE06_24875"
     CDS             2379..2645
                     /locus_tag="QPE06_RS24875"
                     /old_locus_tag="QPE06_24875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001243419.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224471576.1"
                     /translation="MVKLLLVRNEYFNKNNDLKTVARFDGKTLRDAFSRKIATFDGKVL
                     RDASLKKVATFDGQNLRDASSKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     Typing          1585..1823
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.934"
                     /coverage="100.0"
                     /evalue="1.67e-114"
     Typing          complement(712..1120)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.512"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          1833..2152
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="4.85e-62"
ORIGIN
        1 gtaccatgat ttatggaata gatgctctgg caaggttgct caaatgtcga ggcttgggca
       61 tgtccaggcg gttgaattga gggcgattct ttctgagata atgccagttt atgatgatta
      121 caagatatct aaattaaagt tgatggctaa gcactatcta aataagttta cgccgccttt
      181 aactgatgat cagattagga aaatagatag gatgctctat gattttgata tagtagggcg
      241 gactaataag aatcttgcaa aactatatag acgtaagctc gtggcattac ttccagatag
      301 gtgattatat ggaaaatgga tttgttaatt tttatgacca tgttaaaggg tatggcttta
      361 taaggcgtga gcgtggacgt gatgttttct ttcggtatga tgattttttg tttttagggc
      421 atgatgtcga tatatgtaaa ggtattttag ttaggtttaa attagaaaaa acagataaag
      481 ggtttaaagc tgtagcgatt caaaaggtat aacatcgtgg atgtgtcagc ttgtttttat
      541 gatatgagaa cttgagatcc tttctatctc gtcgtaatct cttgctgtgt aaacgaaaaa
      601 accgccttgc agggcggttt ttcgaaggtt ctcagagcta ccaactcttt gagccgaggt
      661 aactggcttg gaggagcgca gtcaccaaaa cttgttcttt cagtttagcc ttaacaggcg
      721 catgacttca aggctaactc ctctaattcg gttaccagtg gctgctgcca gtggcgataa
      781 gtcgtgtctt ctcggtttgg attcaagtcg atagttaccg gataaggcgc agcggtcgga
      841 ctgaacgggg ggttcgtgca tacagtccag cttggagcga acgacctaca ccgggccgag
      901 ataccaacag cgtgagctat gagaaagcgc cacgtttccc gaagggagaa aggcggacag
      961 gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa
     1021 cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt
     1081 gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcggcgtgg ccttttccgg
     1141 tcgtgctttt ttgctcacat gttctgtccc ggttatcccc tgattctgtg gataaccgca
     1201 ttaccgtctt tgagtgggct gataccgctc gccgcagccg aacggccgag cgcagcgagt
     1261 cagtgagcga ggaagcggaa aagtgcctga tgtagcattt tctccttacg cacaggtata
     1321 ccattctgca tcctgtctgg tgccggatat actgttatac cccggtgcca ttttccgctt
     1381 caaagcgtgt ctgtatgctg ttctggagtt cttccgcgag ttcgtgcagc ttctcacaca
     1441 tggcggcctg ttcgtcggca tcgagtgcgt ccagcttttc gagcagtgcc aggctctggc
     1501 tttttatgaa tcctgccatg ttgagtacgg cttgctgctg cttgttcatc ttttcgtttt
     1561 ctccgttctg tctgtcatct gcgttgtgtg attatatcgc gtaccacttt tcgactgttt
     1621 taccgccggt attctgccgt ctgacgcttt gacgggcatt tctgccgaca atactgtcac
     1681 tgccaaaaaa ctgccgtgcc tttgtcggta attcgagctt gctgacagga caggatgtgc
     1741 aattgttata ccgcgcatac atgcacgcta ttacaattgc cctggtcagg gctttgcccc
     1801 gacacccatg tcagatacgg agccatgttt tatgacaaaa cgaagtggaa gtaatacgcg
     1861 caggcgggct atcagtcgcc ctgttcgtct gacggcagaa gaagaccagg aaatcagaaa
     1921 aagggctgct gaatgcggca agaccgtttc cggtttttta cgggcggcag ctctcggtaa
     1981 gaaagttaac tcactgactg atgatcgggt actgaaagaa gttatgagac tgggggcgtt
     2041 acagaaaaaa ctctttatcg acggcaagcg tatcggggac agggagtatg cggaggtgct
     2101 gatcgctatt acggagtatc accgggccct gttatccagg cttatggcag attagcttcc
     2161 cggagagaaa ctgtcgaaaa cagacggtat gaacgccgta agcccccaaa ccgatcgcca
     2221 ttcactttca tgcatagcta tgcagtgagc tgaaagcgat cctgacgcat ttttccggtt
     2281 taccccgggg aaaacatctc tttttgcggt gtctgcggca gaatcgcgtt cagcgcgttt
     2341 cagcggtgcg tacaattaag ggattatggt aaatacaatt ggttaaatta ctattggtga
     2401 gaaatgaata tttcaataaa aacaatgact taaaaaccgt tgctcggttt gacggtaaaa
     2461 ccttaagaga tgccttttcg agaaaaatag cgacttttga tggcaaggtt ttaagggatg
     2521 cctctttaaa aaaagtagca acctttgacg gtcagaattt aagagatgct agttcaaaaa
     2581 ttatcctgag tgccgatgct gaggttggga ttgttgttat ggcctttgta gctgagttga
     2641 tttgaatctc atgctgcata ccttttagcc tatcgctggc aggataaggc gctttcttgt
     2701 tggtgacaga aagataaaaa actttataat aatcagcgaa gcgggcgaac cacgcctggc
     2761 tctcgctctt taacaaatgg ttacgtgtat gttgcgcaag gaaaccgatg ccttgttttt
     2821 aaggcgatct cgcatgagat catgaccggc ctggccgcta attaatggtg agaacgcccc
     2881 tgagcgtgta tcagcactaa aagaatagcg acgattgtct ggcaatgtga gttaaaagtc
     2941 ccaaagagcc aatagagttt ttccttgctt tcctactggt ctggcaaaat ttcataacca
     3001 ataggagttg catcatgttt attatcaaca tcaacattaa cgtaaccaag agctcttcat
     3061 cttgttctgg agacggtcag atgaagaaaa aaagagaggt tggctctctg gaggcactga
     3121 aaaaaacaca gtttttgttt tctatgtgct tgattatgtt taaagtaata gattacgtat
     3181 cgaaactttt taactaatcg acttttaact caaacatcat gaataaaccc aggtttaatg
     3241 gaactcctgt tgcatctttg gattctttat ctgcgatgtt aggcatagaa agaaaaagat
     3301 tggactggat agtcaagtct gtatcgatgt cgtacaagca gtttaaggtt gaaacaggga
     3361 agaataaaaa agaaaggcaa atttttgaac ccaagagatc tttgaaagga attcaaaaaa
     3421 aaataaataa agagattttt gagaaaattg attaccctca ttatttgcat ggggcgttaa
     3481 gtggtcgcga ttatatatct aatgccgctg ttcatactag gaaaagaaca gttatatgtc
     3541 ttgatatcac caatttttat cccagcatta gtaaaaaaga tgtttgttct atttttaaaa
     3601 atttaatgcg tttttctcct gatgtttctt tatgcttaac ggaacttgtg acgttgaata
     3661 ataaggtccc tcagggtggg tgctgttcta gttatattgc aaatctttta ttttttaata
     3721 gtgagtataa tctctataat agattgaagt ctatggggct ttcatattca aggcttttag
     3781 atgatattac tatatcttct gataaggatc tttcatcaga ggaaaaaaca aaagtaataa
     3841 aactcgttca cggaatggtg aatcagtaca gactttcaat aaatgaaagt aagacaacga
     3901 tagagcactc aaaagattcg tcttctaaac ttagtgtcac tgggttgtgg gtaaagcatg
     3961 gtgttcctaa gttaacaaaa gaaaatagac gttatatcag gtacttagtt tatatatgta
     4021 aaaaacaagg tgcttatgaa cgtcatacga aaga
//
