GenomeNet

Database: RefSeq
Entry: NC_009344
LinkDB: NC_009344
Original site: NC_009344 
LOCUS       NC_009344               8953 bp    DNA     circular CON 10-MAR-2020
DEFINITION  Shigella dysenteriae Sd197 plasmid pSD197_spA, complete sequence.
ACCESSION   NC_009344
VERSION     NC_009344.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02603600
            Assembly: GCF_000012005.1
KEYWORDS    RefSeq.
SOURCE      Shigella dysenteriae Sd197
  ORGANISM  Shigella dysenteriae Sd197
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 8953)
  AUTHORS   Yang,F., Yang,J., Zhang,X., Chen,L., Jiang,Y., Yan,Y., Tang,X.,
            Wang,J., Xiong,Z., Dong,J., Xue,Y., Zhu,Y., Xu,X., Sun,L., Chen,S.,
            Nie,H., Peng,J., Xu,J., Wang,Y., Yuan,Z., Wen,Y., Yao,Z., Shen,Y.,
            Qiang,B., Hou,Y., Yu,J. and Jin,Q.
  TITLE     Genome dynamics and diversity of Shigella species, the etiologic
            agents of bacillary dysentery
  JOURNAL   Nucleic Acids Res. 33 (19), 6445-6458 (2005)
   PUBMED   16275786
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 8953)
  AUTHORS   Yang,J., Yang,F., Chen,L. and Jin,Q.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAR-2007) State Key Laboratory for Moleclular
            Virology and Genetic Engineering, Microbial Genome Center of
            Chinese Ministry of Public Health, 100 YingXin Street, XuanWu,
            Beijing 100052, P.R.China
COMMENT     REFSEQ INFORMATION: The reference sequence was derived from
            CP000640.
            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/
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/10/2020 06:53:49
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Genes (total)                     :: 4,854
            CDSs (total)                      :: 4,741
            Genes (coding)                    :: 3,646
            CDSs (with protein)               :: 3,646
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 1,095
            CDSs (without protein)            :: 1,095
            Pseudo Genes (ambiguous residues) :: 0 of 1,095
            Pseudo Genes (frameshifted)       :: 488 of 1,095
            Pseudo Genes (incomplete)         :: 525 of 1,095
            Pseudo Genes (internal stop)      :: 240 of 1,095
            Pseudo Genes (multiple problems)  :: 143 of 1,095
            ##Genome-Annotation-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..8953
                     /organism="Shigella dysenteriae Sd197"
                     /mol_type="genomic DNA"
                     /strain="Sd197"
                     /serotype="1"
                     /db_xref="taxon:300267"
                     /plasmid="pSD197_spA"
     gene            join(<8858..8953,1..147)
                     /locus_tag="SDY_RS24195"
                     /pseudo
     CDS             join(<8858..8953,1..147)
                     /locus_tag="SDY_RS24195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000787081.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
     gene            741..1697
                     /locus_tag="SDY_RS24200"
                     /old_locus_tag="SDY_PA01"
     CDS             741..1697
                     /locus_tag="SDY_RS24200"
                     /old_locus_tag="SDY_PA01"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001293214.1"
                     /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_001293214.1"
                     /translation="MSELVVFKANELAVSRYDLTEHETKLILFCVAKLNPTIENPTRD
                     ELTVKFSCSEYARTMGLSYENAWGRLNSATSDLFKRSVELIYPTGAVSKRIFNWTEYA
                     EFNREEQTVTLVFSSYIQPLLFHLKKFIKYNLEHVKAFENKYSMRIYEWLLKELSQRK
                     THRGNIEISIKEFKFMLMLEKNYPLYAELNRWILKPVTNDLNTYSNMKLTIEKRGRPA
                     DTLIFQVELDKQIDLVTELAKDPASKKEDKTIRLTPENRLHEGLKTTLHDALTAKIQL
                     TSFEAKFLSDMQSKYDLNGSFTWLTQKQRTTLEKILAKYGRI"
     gene            1705..>2016
                     /locus_tag="SDY_RS24205"
                     /pseudo
     CDS             1705..>2016
                     /locus_tag="SDY_RS24205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006816427.1"
                     /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="DNA-binding protein"
     gene            2073..2770
                     /locus_tag="SDY_RS24210"
                     /pseudo
     CDS             2073..2770
                     /locus_tag="SDY_RS24210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
     gene            complement(2979..4112)
                     /locus_tag="SDY_RS24215"
                     /old_locus_tag="SDY_PA04"
     CDS             complement(2979..4112)
                     /locus_tag="SDY_RS24215"
                     /old_locus_tag="SDY_PA04"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glycosyltransferase family 4 protein"
                     /protein_id="WP_000703236.1"
                     /translation="MKISIIGNTANAMILFRLDLIKTLTKKGISVYAFATDYNDSSKE
                     IIKKAGAIPVDYNLSRSGINLAGDLWNTYLLSKKLKKIKPDAILSFFSKPSIFGSLAG
                     IFSGVKNNNAMLEGLGFLFTEQPHGTPLKTKLLKNIQVLLYKIIFPHINSLILLNKDD
                     YHDLIDKYKIKLKSCHILGGIGLDMNNYCKSTPPTNEISFIFIARLLAEKGVNEFVAA
                     AKKIKKTHPNVEFIILGAIDKENPGGLSESDVDTLIKSGVISYPGFVSNVADWIEKSS
                     VFVLPSYYREGVPRSTQEAMAMGRPILTTNLPGCKETIIDGVNGYVVKKWSHEDLAEK
                     MLKLINNPEKIISMGEESYKLARERFDANVNNVKLLKILGIPD"
     gene            complement(4112..4920)
                     /locus_tag="SDY_RS24220"
                     /old_locus_tag="SDY_PA05"
                     /pseudo
     CDS             complement(4112..4920)
                     /locus_tag="SDY_RS24220"
                     /old_locus_tag="SDY_PA05"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000788525.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="glycosyltransferase family 2 protein"
     gene            complement(4917..6022)
                     /locus_tag="SDY_RS24225"
                     /pseudo
     CDS             complement(4917..6022)
                     /locus_tag="SDY_RS24225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000538728.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
     gene            6194..>7025
                     /locus_tag="SDY_RS24230"
                     /pseudo
     CDS             6194..>7025
                     /locus_tag="SDY_RS24230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001080803.1"
                     /note="frameshifted; internal stop; 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="oligosaccharide flippase family protein"
     gene            7083..>7148
                     /locus_tag="SDY_RS24235"
                     /pseudo
     CDS             7083..>7148
                     /locus_tag="SDY_RS24235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012477181.1"
                     /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="hypothetical protein"
     gene            7225..7497
                     /locus_tag="SDY_RS24240"
                     /old_locus_tag="SDY_PA07"
     CDS             7225..7497
                     /locus_tag="SDY_RS24240"
                     /old_locus_tag="SDY_PA07"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_145811.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000019161.1"
                     /translation="MSHNLEHQKVHTRMVKEVLKAVARANNHPYQSVFTDFIAGHPSC
                     TVCFWETFHKMSPDSPYEYVTFCHTCRRFDLYETEAEMKADDPKWW"
     gene            7478..8686
                     /locus_tag="SDY_RS24245"
                     /old_locus_tag="SDY_PA08"
     CDS             7478..8686
                     /locus_tag="SDY_RS24245"
                     /old_locus_tag="SDY_PA08"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000198547.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="WP_000198563.1"
                     /translation="MTRSGGDFQPRPLKRLFTTNQCWTSFLDASGLRDIEVEAVTKML
                     ACGTRILGVKEYNCDKPECPHVRYVTNSCGSRACPSCGKKATDLWIATQLNRLPDCDW
                     VHLVFTLPDTLWPVFESNRWLLNDVCRLAVENLLYAARKRGQEPGIFCAIHTYGRRLN
                     CHPHVHVSVTCGCLNKHGQWKKLSFLKDAMRSRWMWNMRQLLLKAWSEGLAMPESLSH
                     ITTESQWRSLVLKAGGKYWHVYMSKKTAGGRNTARYLGRYLKKPPIAASRLAHYNGGA
                     SLSFRYLDHKTGETAMETLTQRELVARLKQHIPEKFFKMVRYFGFLANRVCGEKLPQV
                     YRALGMDKPAPVAKVCYAQMVKQFLSRDPFECVLCGGRMVYRRAIAGLNVEGLKKNAR
                     DISLLRYMPA"
CONTIG      join(CP000640.1:1..8953)
//
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