LOCUS       NZ_CP045787             2679 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Shigella dysenteriae strain CFSAN029786 plasmid p3CFSAN029786,
            complete sequence.
ACCESSION   NZ_CP045787
VERSION     NZ_CP045787.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04323531
            Assembly: GCF_009662135.1
KEYWORDS    RefSeq.
SOURCE      Shigella dysenteriae
  ORGANISM  Shigella dysenteriae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2679)
  AUTHORS   Mafiz,A., Kastanis,G. and Gonzalez Escalona,N.
  TITLE     Closed genomes of twenty-eight foodborne pathogens from the CFSAN
            verification set by a combination of long and short-reads
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2679)
  AUTHORS   Mafiz,A., Kastanis,G. and Gonzalez Escalona,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-NOV-2019) ORS/DM/MMSB, Food and Drug
            Administration-College Park, 5001 Campus Drive, College Park, MD
            20740-3835, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes, CANU v. 3.12.0, 1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 176, 244, 292, 244, 227x
            Sequencing Technology :: Oxford Nanopore GridION, Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009662135.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 03:57:13
            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)                     :: 5,212
            CDSs (total)                      :: 5,085
            Genes (coding)                    :: 4,226
            CDSs (with protein)               :: 4,226
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 99
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 859
            CDSs (without protein)            :: 859
            Pseudo Genes (ambiguous residues) :: 0 of 859
            Pseudo Genes (frameshifted)       :: 266 of 859
            Pseudo Genes (incomplete)         :: 578 of 859
            Pseudo Genes (internal stop)      :: 164 of 859
            Pseudo Genes (multiple problems)  :: 135 of 859
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045787.1.
            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..2679
                     /organism="Shigella dysenteriae"
                     /mol_type="genomic DNA"
                     /strain="CFSAN029786"
                     /serovar="Serotype 3"
                     /host="Homo sapiens"
                     /db_xref="taxon:622"
                     /plasmid="p3CFSAN029786"
                     /geo_loc_name="Somalia"
                     /collected_by="FDA"
     gene            complement(469..663)
                     /locus_tag="GH770_RS25695"
                     /old_locus_tag="GH770_25695"
     CDS             complement(469..663)
                     /locus_tag="GH770_RS25695"
                     /old_locus_tag="GH770_25695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041639.1"
                     /translation="MNKQQQTVLNMAGFIKGQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            947..1270
                     /gene="mobA"
                     /locus_tag="GH770_RS25700"
                     /old_locus_tag="GH770_25700"
     CDS             947..1270
                     /gene="mobA"
                     /locus_tag="GH770_RS25700"
                     /old_locus_tag="GH770_25700"
                     /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_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1496..2119)
                     /locus_tag="GH770_RS25705"
                     /old_locus_tag="GH770_25705"
     CDS             complement(1496..2119)
                     /locus_tag="GH770_RS25705"
                     /old_locus_tag="GH770_25705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005112197.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_252866734.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQSIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(2499..2660)
                     /locus_tag="GH770_RS26700"
     CDS             complement(2499..2660)
                     /locus_tag="GH770_RS26700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     Typing          699..938
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.17"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          complement(2..440)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.034"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2511..2679)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.353"
                     /coverage="100.0"
                     /evalue="2.12e-61"
     Typing          948..1267
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="6.59e-62"
ORIGIN
        1 acgacctaca ccgaactgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc
       61 gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg
      121 agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc
      181 tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
      241 acctgcgcgg cctttgtccc tgccttcggc tttttgctca catgctcttt ccggcgttat
      301 cccctgattc tgtggataac cgcattaccg cctttgagtg agctgacacc gctcgccgca
      361 gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc cttatgtgac
      421 attttctcct tacgctctgt tgtgccgttc ggcatcctgt cctgagcgtt atctctctgt
      481 gctattttct acttcaaagc gtgtctgtat gctgttctgg agttcttctg cgagttcgtg
      541 cagcttctca cacatggtgg cctgctcgtc agcatcgagt gcgtccagtt tttcgagcag
      601 cgtcaggctc tggcctttta tgaatcccgc catgttgagt acggtttgct gctgcttgtt
      661 catcttttcg ttttctccgt tctgtctgtc atctgcgtta tgtgattata tcgcgtacca
      721 cttttcgact gttttgctgc cgctattctg ccgcctggct ttttgacggg catttctgtc
      781 agacaacact gtaactgcca aaaaactgcc gtgcctttgt cggtaattcg agcttgctga
      841 caggacagga tgtgcaattg ttataccgcg catacatgca cgctattaca attgccctgg
      901 tcagggcttt gccccgacac ccatgtcaga tacggagcca tgttttatga caaaacgaag
      961 tggaagtaat acgcgcaggc gggctatcag tcgccctgtt cgtctgacgg cagaagaaga
     1021 ccaggaaatc agaaaaaggg ctgctgaatg cggcaagacc gtttccggtt ttttacgggc
     1081 ggcagctctc ggtaagaacg ttaactcact gactgatgat cgggtactga aagaagttat
     1141 gagactgggg gcgttacaga aaaaactctt tatcgacggc aagcgtatcg gggacaggga
     1201 gtatgcggag gtgctgatcg ctattacgga gtatcaccgt gccctgttat ccaggcttat
     1261 ggcagattag cttcccgggg agaaaactgt tgaaaacaga cggtatgaac acggtaagct
     1321 cccaaagtga tctccattcg ctttcatgca tagctatgca gcgagctgaa aacgatcctg
     1381 acgcatcctt cctgtttttc cggggtaaaa catctatttt tgtggtgtct gcgtcagaat
     1441 cgcgttcagc gcgtttcagt ggtgcgtaca attaagggat tatggtaaat gatgattatt
     1501 tctcctctct atttactcgg caagcgccaa agtgaattac atcatatttt actcctgatt
     1561 catttattac tttaaatatg tcagaaaggt gcttcttatg atttttatca gttataaatg
     1621 ctatatcaat atttttgttt cctaagccat cttgatgtct ttgtataata ttttgggctt
     1681 gttcatggta atatagagca tagtttttta tcttctcatt acttgttgcg tattcttttc
     1741 tatatatgga ttgtgacatc atttcttctt ctaattttga ttgaggtata ttgcgcgcgt
     1801 tcgctagaac ttttaggtca tctttgctta tgtttagtga tggtgttaac cctttttgag
     1861 cttcagtatg gcgtttgttt acctctgaaa gaacgcttag tccctttgtg aagtcgttgt
     1921 cttttgtata aaaatcaatt cttaggtttt tggggactac agtccatcca tcgccttttt
     1981 gacgcgtgaa tagtgtttgt ggatgggaga tctctttcca tccaccatgc gacataatga
     2041 caagttgtgt tgcttttcct gtttggctca atcctattcc gtctttctgg aataaacgac
     2101 gatgacttgt tacgtccatg tttggtgatg ggtgtgtttt tatatttttg gatgatgtta
     2161 gaaggtgatt tcttattgtt gatgatatgt ttgttatgag attcgaattg agtattttca
     2221 tttgttaaca atccattttt gcggtgtttt ttattgtttt tttttctttt gtttaagggc
     2281 gtgtcggtgt aagtgtttat tttatgggtt aaagtaggat accaagtgtg aaaaaaaatt
     2341 aaaggttctt cttgagatcc tttttttctg cgcgtaatct actgcctgta aacgaaaaaa
     2401 ccgccctgca aggcggtttt tcgaaggttc tcagagctac caactctttg agccgaggta
     2461 actggcttgg aggagcgcag tcaccaaaac ttgttctttc agtttagcct taacaggcgc
     2521 atgacttcaa gtcttactcc tctaattcgg ttatcagtgg ctgctgccag tggcgataat
     2581 tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc
     2641 tgaacggggg gttcgtgcac acagcccagc ttggagcga
//
