LOCUS       NZ_CP045786             4065 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Shigella dysenteriae strain CFSAN029786 plasmid p2CFSAN029786,
            complete sequence.
ACCESSION   NZ_CP045786
VERSION     NZ_CP045786.1
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 4065)
  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  JOURNAL   Unpublished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 4065)
  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
            CP045786.1.
            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..4065
                     /organism="Shigella dysenteriae"
                     /mol_type="genomic DNA"
                     /strain="CFSAN029786"
                     /serovar="Serotype 3"
                     /host="Homo sapiens"
                     /db_xref="taxon:622"
                     /plasmid="p2CFSAN029786"
                     /geo_loc_name="Somalia"
                     /collected_by="FDA"
     gene            48..161
                     /locus_tag="GH770_RS26690"
     CDS             48..161
                     /locus_tag="GH770_RS26690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            562..915
                     /locus_tag="GH770_RS25665"
                     /old_locus_tag="GH770_25665"
     CDS             562..915
                     /locus_tag="GH770_RS25665"
                     /old_locus_tag="GH770_25665"
                     /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="WP_252866920.1"
                     /translation="MVNSLLKERIIHSPKELEHDNAVIRALQKLQIQEVCNSTLWETAK
                     QQLLQKSDGRYFAINSKHLAFPGPGESHAFCCIKYKNAIGINGNNAETQSTHYQPYPYD
                     KVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(1385..1618)
                     /locus_tag="GH770_RS25670"
                     /old_locus_tag="GH770_25670"
     CDS             complement(1385..1618)
                     /locus_tag="GH770_RS25670"
                     /old_locus_tag="GH770_25670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137429.1"
                     /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_000137430.1"
                     /translation="MTELEMHLLNALEQLQQDYTQRLKDWESAFTDLQHMFELTRQENG
                     QLREQCDDLSQQVQRLVEQVDHLSRLFITNSR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1625..2185)
                     /locus_tag="GH770_RS25675"
                     /old_locus_tag="GH770_25675"
     CDS             complement(1625..2185)
                     /locus_tag="GH770_RS25675"
                     /old_locus_tag="GH770_25675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067489.1"
                     /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_000067489.1"
                     /translation="MSNLLQMGTDFEKKLKERAVSTENILNSEFRKLEASVDRELNLNG
                     QKIRDAISAHTAAVKEQLETLNSAVNAQFSATENELARRQEELLWKLVKGRILYPSLTA
                     LCVTGGIFLASWGLIQWQESRIAANILAIRDQEETLAKLREKTWGVTYHEGRNGKFLVL
                     PSGVKGENNWTVEKKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2220..2900)
                     /locus_tag="GH770_RS26950"
                     /old_locus_tag="GH770_25680"
                     /pseudo=""
     CDS             complement(<2220..2900)
                     /locus_tag="GH770_RS26950"
                     /old_locus_tag="GH770_25680"
                     /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(2863..3186)
                     /locus_tag="GH770_RS25685"
                     /old_locus_tag="GH770_25685"
     CDS             complement(2863..3186)
                     /locus_tag="GH770_RS25685"
                     /old_locus_tag="GH770_25685"
                     /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_001444404.1"
                     /translation="MLTIRVTDEEHARLLARCEGKQLASWMRKVCLGAPPSKTSGLPTL
                     APPLLRQFASVGNNLNQIARKINSGQWSGHDRVHVVAALMAIGRELSELRDEVRKQGER
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3254..3445
                     /locus_tag="GH770_RS25690"
                     /old_locus_tag="GH770_25690"
     CDS             3254..3445
                     /locus_tag="GH770_RS25690"
                     /old_locus_tag="GH770_25690"
                     /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_000165980.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADDQADICEALHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3531..3618)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          2..157
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.43e-70"
     Typing          3629..4065
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.85"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1279..2873)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.06"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3246..3448)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.706"
                     /coverage="100.0"
                     /evalue="3.7e-12"
ORIGIN
        1 gttggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc
       61 ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa
      121 gacacgactt aacgccactg gcagcagcca ttggtaacta gacaaggtgg attgagatat
      181 taagagttct tgaagtggtg gcctaactgc ggctacacta gaaggacagt atttggtatc
      241 tgtgctccac caagccagtt accttcggaa gaaagagttg gtagctctag attccggcaa
      301 acaaaccacc gttggtagcg gtggtttttt tgtttgcagg cagcagatta cgcgccgcaa
      361 aaaaggatct caagaagatc ttgaatcact ctatgaaaat tttgttttat agccgtattt
      421 gttgatgcta taagccagag accttctatg agaatagaca tatcacatca aacacggcat
      481 accccgccaa acatgcttcc tcgggaacaa aattgtgtag caatggcatt atctgcgtgc
      541 tttagacaac aactaaaccc tgtggtaaac agcttattaa aagagagaat aatacactcc
      601 cctaaagaat tggaacatga caacgcagta ataagagccc tgcaaaaact acaaattcaa
      661 gaagtttgta acagcaccct ttgggagaca gccaaacaac aactacttca aaaatcggac
      721 ggaagatatt ttgccatcaa ttctaaacac ttagcctttc caggcccagg agaatctcac
      781 gccttctgtt gcatcaaata caaaaatgca attggcatta acggaaacaa tgccgaaacc
      841 caatcgaccc actaccaacc ctatccctat gataaagtca gtatatgggg accattccct
      901 cacaatttaa cgtaatatct taattgtacg caccgctgaa atgcgttcag cgcgatcacg
      961 gctgctgaca ggtaaaaata gcaacaaacc acccgaaaag ctgccgcgat cgcacctgat
     1021 aaattttaac cgtatgcata gctattcagc catgtgaata acgctggttt tgcctgcgta
     1081 aacctcatga cactgttttt tttccatctt ttcagttgat gacatacgca gacatcgcgg
     1141 gatgaggctg aggaatgagc gcgatctggc aaagaggcaa aacacagcaa caaaaacgac
     1201 acgccagaat cgcgcccgga tgcgttttta acgcgttccg gtaccatctg gcaacctccc
     1261 ggaacaactc accgtcatat ccctattgac gggccacgcc atacccgtgc ttcccgttcc
     1321 tgctcttcat gccaggaccg cgcacgctcc cgttccaggc gtgcctgcct ttcctgttca
     1381 tcccttatct gctgttcgtg ataaataacc gactcaagtg gtccacctgc tcgactaatc
     1441 tctgcacctg ctgactcaag tcgtcgcact gttccctcag ttgcccgttc tcctgtcgtg
     1501 tcagctcgaa catatgctgc aaatccgtga aggcgctctc ccagtctttc agccgctgcg
     1561 tatagtcctg ctgcaattgc tctaaggcgt tcagtaagtg catttccagc tctgtcatac
     1621 tcacttactc cctgaccagt cttactgcgt tcttcttctc caccgtccag ttgttttccc
     1681 ccttcacccc ggacggcaat accagaaatt tcccgttcct gccctcgtga tacgtcacac
     1741 cccatgtttt ttcccggagt ttcgccagcg tctcttcctg gtccctgata gccaggatgt
     1801 tcgccgcaat ccggctttcc tgccactgaa tcagccccca tgacgccaga aaaatcccgc
     1861 ccgtgacgca aagcgccgtc agcgacgggt acagtatccg ccctttgacc agcttccaga
     1921 gcagctcttc ctgccgccgg gccagttcgt tctctgtggc gctgaactgc gcgttcacgg
     1981 cactgttcag cgtctccagt tgttctttca ccgctgctgt gtgtgcgctg atagcgtctc
     2041 tgattttctg cccgtttaag ttcagttccc tgtctacaga cgcttcgagc ttcctgaact
     2101 cgctgttcag tatgttctct gtagagacgg cacgctcttt cagtttcttc tcgaagtctg
     2161 tccccatttg taaaagattg ctcatacagc gcccctttca gcctgagatt acgcccgccc
     2221 tccgggtcgg cgatactgat actgctcctg gttgtcctca caacctcaaa acctgccgct
     2281 gtaagcgcct cagtgacatc ctgacgcgtt tttagcgctc cggcatggta aagagcctcc
     2341 agtcccctcg taatcgcttc tgcggcctcc tgtttcgctt tcggcagatt attcggggtg
     2401 acaagtgtcc gcctgttctc cggtgcgttc gggtcgtgca gcccgtaatg gtgattcacc
     2461 agtgtctgcc aggcattgat tcgcggacgg tccgctcggt cgtaataggg ctggagccgt
     2521 tttccgctcg ccagctccat attcgggatg acaaaattca gctcaagacg ccccttgtcc
     2581 tggtgctcca cccacaggat gctgtactga tttttttcaa gaccgggcat cagtacccgc
     2641 tcaaagctct ccatcaccct ttcacgctct cccggtggca gggtctgctc tgcaaaagac
     2701 agaacccccg aggtgtattt tttcgcaaac ggcgtagcat cgatgagttc ccgcacctct
     2761 tcgggagcac cccgcagaac tctcgcccct tcccggttac gctcccggcc cagcaggtaa
     2821 tcaaccggac cactgccacc gccttttccc ctggcatgaa acttaactat catcccgctc
     2881 tccctgttta cggacctcat ccctcagctc actcagttca cgtccgatgg ccatcagtgc
     2941 agccaccaca tgaacccggt catgccccga ccactgtccg ctgtttatct tccgggctat
     3001 ctgattcagg ttattgccga ccgaagcgaa ctggcgcaac agcggcggtg ccagtgtcgg
     3061 aagacctgac gttttcgatg gcggtgcccc caggcagacc ttacgcatcc atgacgcaag
     3121 ttgttttccc tcacaacgtg ccagcagccg cgcatgttcc tcatccgtga cccgtatcgt
     3181 gagcatcctt tcgcgtttca ccggtatcat taaaaacctc cgacagactc cccacacatg
     3241 gagaaacaga actgtgacta aacaggaaaa aaccgccctt aacatggccc gcttcatcag
     3301 aagccagacg ctgaccctgc tggaaaaact gaatgaactg gacgccgacg accaggctga
     3361 catctgcgaa gcgcttcacg accacgctga cgagctttac cgcagctgcc tcgcacgctt
     3421 cggggatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca cagctggcct
     3481 gtgagcggat gccgggagca gacaagcccg tcagggcgcg tcagcaggtt ttagcgggtg
     3541 tcggggcgca gccatgaccc agtcacgtag cgatagcgga gtgtatactg gcttaatcat
     3601 ttggcatcag tgaggattgt atgaaaagtg caccatgccg ggtgtgaaat gccgcacaga
     3661 tgcgtaagga gaaaatgctc gtccaggcgc ttttccgctt cctcgctcac tgactcgctc
     3721 cgctcggtcg ttcggctgcg gcgagcggta tcagctcact caaagacggt aatgcggtta
     3781 tccacagaat caggggataa caccaaaaga aacatgtgag caaaaaacaa gaacccggaa
     3841 aaggccacgc agctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat
     3901 cgacgctcaa gtcagaggtg gcgaaacccg acaggactta aagataccag gcgtttcccc
     3961 ctggtggctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg
     4021 cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgct
//
