LOCUS       NZ_CP034069             5034 bp    DNA     linear   CON 16-APR-2024
DEFINITION  Shigella sonnei strain FDAARGOS_524 plasmid unnamed3.
ACCESSION   NZ_CP034069
VERSION     NZ_CP034069.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163218
            Assembly: GCF_003855115.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5034)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5034)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-NOV-2018) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 2.3.0, HGAP v. 3.0, SPAdes v. 3.6.0
            Genome Coverage                   :: 1000.9613794x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003855115.1-RS_2024_04_16
            Annotation Date                   :: 04/16/2024 11:34:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,040
            CDSs (total)                      :: 4,907
            Genes (coding)                    :: 4,266
            CDSs (with protein)               :: 4,266
            Genes (RNA)                       :: 133
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 641
            CDSs (without protein)            :: 641
            Pseudo Genes (ambiguous residues) :: 0 of 641
            Pseudo Genes (frameshifted)       :: 184 of 641
            Pseudo Genes (incomplete)         :: 434 of 641
            Pseudo Genes (internal stop)      :: 110 of 641
            Pseudo Genes (multiple problems)  :: 84 of 641
            Pseudo Genes (short protein)      :: 3 of 641
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034069.1.
            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/
FEATURES             Location/Qualifiers
     source          1..5034
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_524"
                     /isolation_source="Stool"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_524"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /collection_date="2015-12-29"
                     /collected_by="Children's National Hospital"
     gene            <1..111
                     /locus_tag="EGX92_RS26295"
     CDS             <1..111
                     /locus_tag="EGX92_RS26295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_250187176.1"
                     /translation="HEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="replication initiation protein"
     gene            517..906
                     /locus_tag="EGX92_RS25370"
                     /old_locus_tag="EGX92_25415"
     CDS             517..906
                     /locus_tag="EGX92_RS25370"
                     /old_locus_tag="EGX92_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(970..1254)
                     /locus_tag="EGX92_RS25375"
                     /old_locus_tag="EGX92_25420"
     CDS             complement(970..1254)
                     /locus_tag="EGX92_RS25375"
                     /old_locus_tag="EGX92_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(1272..1469)
                     /locus_tag="EGX92_RS25380"
                     /old_locus_tag="EGX92_25425"
     CDS             complement(1272..1469)
                     /locus_tag="EGX92_RS25380"
                     /old_locus_tag="EGX92_25425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            1681..1977
                     /locus_tag="EGX92_RS25385"
                     /old_locus_tag="EGX92_25430"
     CDS             1681..1977
                     /locus_tag="EGX92_RS25385"
                     /old_locus_tag="EGX92_25430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            complement(2522..2755)
                     /locus_tag="EGX92_RS25475"
     CDS             complement(2522..2755)
                     /locus_tag="EGX92_RS25475"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2762..3292)
                     /locus_tag="EGX92_RS25480"
     CDS             complement(2762..3292)
                     /locus_tag="EGX92_RS25480"
                     /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_015386306.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3330..4028)
                     /locus_tag="EGX92_RS26300"
                     /pseudo=""
     CDS             complement(<3330..4028)
                     /locus_tag="EGX92_RS26300"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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(3970..4293)
                     /locus_tag="EGX92_RS25405"
                     /old_locus_tag="EGX92_25445"
     CDS             complement(3970..4293)
                     /locus_tag="EGX92_RS25405"
                     /old_locus_tag="EGX92_25445"
                     /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_000956005.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4358..4549
                     /locus_tag="EGX92_RS25410"
                     /old_locus_tag="EGX92_25450"
     CDS             4358..4549
                     /locus_tag="EGX92_RS25410"
                     /old_locus_tag="EGX92_25450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4635..4721)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.47e-38"
     Typing          complement(2419..3980)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.616"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
       61 aacccggtaa gacacgactt aacgccactg gcagcagcca ttggtaacta aaaagtggat
      121 ttagatacgc agaactcttg aagttgaagc cttatagcgg ctacactgaa aggacatctt
      181 ttggtatctg tgctccactt aagccagcta cccggttagg taatctgcca ggattagcta
      241 accttcgaaa aaccacctgc cagggtggtt ttttcgttta caggcagcag attacgcgca
      301 gaaaaaaagg atctcaagaa gatcctttga tcttttttct ctaaactgca atcccatcag
      361 ttcaggagag aaagatagta taattgccct ctcttatatg gaaccaccat tcaatcacat
      421 catgggaata atataagtga aaacgttcgc attgtttatt tttacgtgta tatgtattta
      481 tagattggaa ttttaacaaa ataaaatgga gttaatatgt tcaaatcatc agtaaagtca
      541 ataacatcga gtactatact gaccttactt ataggatgtt caagtactga aacaaacaaa
      601 aacattgttt acaaagttgg tggtgacagc atcattctga ataaatattg catacttaaa
      661 atgtaccctt cccaatcaga aaaaaacaaa ggcgtcataa tagaagtaaa cacagatagt
      721 ttatgtaaga aaaaactaaa cgaaataact agtaaaaata tagggaaacc cctgatttca
      781 tattttgatg gaaaagtaat atcccaacct gcaatcattc attctgcact aaatccaacc
      841 cattattatc aacctgtgaa cgatgaaaca acagtgatgg aaatcataaa agcatattca
      901 aaataatatt aatagatata atcctgctta aggtatagct taggcaggat tatatctatt
      961 cagctcttat tataaggtag tgtatacatg aataatctgc cctgtcccac tgacactttt
     1021 aaatttaatt ttatcaacac cagcgccctt gcaagagatc tgataagatg ctggaccaat
     1081 aacgttaact gttcttggcc cattaggggc ataccagata aaagcaataa atggaccggg
     1141 tacattagac aatgtatcaa aatagacagt gtacgcgata tcaccagtat gattttcaag
     1201 ttcaacccaa ggaccaaaaa agaaaggagg agcccaaaca ttttgagaaa tcatataatc
     1261 tcctgattag ttcaatgcga atgttcttcc cattcactct cgcaagaaac atctataagc
     1321 tcaacatcta gcccactaac agaatcagag aaatacttat aaacatcatc ccttgttccc
     1381 ataaggtctg ccgaacatga tagttcacaa ccattcttat tcctaactac aaataagaaa
     1441 cggtgaagca atactttttc ttctttcatt ttatccctcc ctttatttac acagaatata
     1501 ctgtatatat aaatactagt tttatataca gtataaatta cgccgcatta tttttcctgt
     1561 caatgatatg aattttcatt tttgtgatct gaatcaccct tataaaaatc aggaagggaa
     1621 gattcgcagc agaaaaacag caccggataa catcaggaga aaaaacagag aggagataac
     1681 gtgagcaaaa caaaatctgg tcgccaccga ctgagcaaaa cagacaaacg cctgctggct
     1741 gcacttatcg ctgccggata cgaagagcgg acagcccgtg acctcatcca gaaacacgtt
     1801 tacacactga cacaggccga cctgcgccat ctggtcagtg aaatcagtaa cggtgtggga
     1861 cagtcacagg cctacgatgc gatttaccag gcaagacgca ttcgtctcgc ccgtaaattc
     1921 ctgaacggaa aaaaaccgga agaagggctg aacgcctgga agggtgattt accataatca
     1981 cttattgtac gcaccgctga aacgcgttcg gcgcgatcac ggcagcagac aggtaaaaat
     2041 ggcaacaaac cacccgaaaa actgccgcga tcgtacccgg taaattttaa ccacatgcat
     2101 agctatgcag ctatgtgaat catgcaggaa ttgccagcca gagacagctg aaacggattt
     2161 ttttcatgct ttcggaagcg aagaagacgg ggaccggagc gggaaaacag aagttcaggg
     2221 gaatgagcgc gatctggcaa tagaggcaaa acacagcaac aaaagacaca ccagaatcgc
     2281 gcccgtatgc gttttaacgc gttcctgtgt tttcagcaag gtctgactga agcgcgttcc
     2341 cggtgccccc gaaccaacca ttatcccaaa aaatgcaccg gaaacgcgct gacaacattt
     2401 tagcctgtct ctgattacca tcccagcgaa gggccatcca gtgtccgttc ctgtatttcc
     2461 agctggcgct cacgctccag ggataacgca tgttcgcgtt cctgtatcag ccgttcgtcc
     2521 cttatctcct gttctcgctg tataactggc tcaagcgttc tgtctgctcg ctcaagtgct
     2581 gcacctgctg actcaactgc atgacccgct cgttcagcat cgcgttgtcc cgttgcgtaa
     2641 gcgaaaacat tttctgcaat tccacgaagg cgctctccca ttcgttcagc cgctgcatat
     2701 agtcctgttg cagttgctct aatgcgttca gcaaatgtct ttccagctcc gtcatgctct
     2761 gttactcctg taccagcctt acggcattct gtttcccgtt ttccatcgtc cagttcgttt
     2821 cggctttcat cccctcgggc aacaccagaa aacgtccgtt gctcccctcg tgataacgca
     2881 cgccccatgt cttcgcgttc agcttctcca gattctcgtt ctgcttcctg atttcttcca
     2941 ggttcgcctg tatcatcccg ccaagatacc agagcgtccc gccactcacg gtaaacagga
     3001 aaatgaccat ccccagtaac atcatgcccg tattccctgc cagctttaac acgtccttcc
     3061 tgtgctgcat catcgcctct ttcacccctt cccggtgttt tttcagtgat tcctctgtcg
     3121 aagctgtgaa cagggctata gcgtctttga ttttcgtctc gtttgatgtc acagccttgc
     3181 ttacagattt ttcgagcttc ctgaactcgt cgttcagtat tgtctctgta gattcggctc
     3241 tctctttcag ctttttctcg aactccgcgc ccgtctgtaa aagattgctc ataaaatgct
     3301 cctttcagcc tgatattctt cccaccgttc gggtctgcaa tgctgatact gcttcgcgtc
     3361 accctgacca cttcaagccc tgcctctgtg agcgcctgaa tcacatcctg acggcctttt
     3421 atctccccga catgataaag agcgtctatc ccgcgtgtga cgctctctgc aagcgcctgt
     3481 ttcgtttccg gcaggttatc agagagagtc agtatccggc ggttctccgg ggcgttgggg
     3541 tcatgcagcc cgtaatggtg attcaccagc gtctgccagg catcaattct cggcctgtct
     3601 gcccggtcgt agtacggctg gaggcgtttt ccggtctgta gctccatgtt cggaatgaca
     3661 aaattcagct caagccgtcc cttgtcctgg tgctccaccc acaggatgct gtactgattt
     3721 ttttcgagac cgggcatcag tacacgctca aagctcgcca tcaccttttc acgtcctccc
     3781 ggtggcagct ccttctccgc gaacgacagc acaccggacg tgtatttctt cgcaaatggc
     3841 gtggcatcga tgagttcccg tacttcttcc ggattaccct gaagcaccgt tgccccttcc
     3901 cggttacgct cccttcccag caggtaatca accggaccac tgccaccacc ttttccccgg
     3961 gcatgaaact taactatcat cccgcgtccc ctgttccctg acggccagac gcagccggcg
     4021 cagctcatcc ccgatggcca tcagtgcggc caccacctga acccggtcac cggaagacca
     4081 ctgcccgctg ttcaccttcc tcgctgtctg attcaggtta ttcccgatgg cggccagctg
     4141 acgcagtaac ggcggtgcca gtgtcggcag cctcccggaa cgggcaaccg gctcacccag
     4201 gcagacccgc cgcatccata ccgccagctg tttaccctca cagcgttcaa gtaaccgggc
     4261 atgttcatca tcagtaaccc gtattgtgag catcctctcg cgtttcatcg gtatcattat
     4321 ccccatgaac agaaatcccc cttacacgga ggcatcagtg accaaacagg aaaaaaccgc
     4381 ccttaacatg gcccgcttta taagaagcca gacattaacg ctgctggaga agctcaacga
     4441 actggacgcg gatgaacagg cagatatctg tgaatcgctt cacgaccacg ccgatgagct
     4501 ttaccgcagt tgcctcgctc gcttcgggga tgacggtgaa aacctctaac acatgcagct
     4561 cccggagacg gtcacagctt gtctgtgagc ggatgccggg agctgacaag cccgtcaggg
     4621 cacgtcagcg ggttttagcg ggtgtcgggg cgcagccctg acccagtcac gtagcgatag
     4681 cggagtgtat actggcttaa ccatgcggca tcagtgcgga tggtatgaaa agtgcgccat
     4741 accgggtgtg aaatgccgca cagatgcgta aggagaaaat gcacgtccag ccgcttttcc
     4801 gcttcctcgc tcactgactc gctacgctcg gtcgttcgac tgcggcgagc ggtatctact
     4861 cactcaaaaa cgaaatgctg ttatccacag aatcagggga taacaccgga aaaaacatgt
     4921 gagcaaaaga ccaggaacag gaagaaggcc gcgccgctgg cgtttttcca taggctccgc
     4981 ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccg
//
