LOCUS NC_009344 8953 bp DNA circular CON 03-APR-2025
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; Pseudomonadati; Pseudomonadota; 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 is identical to
CP000640.1.
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/
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Name :: GCF_000012005.1-RS_2025_03_27
Annotation Date :: 03/27/2025 04:02:03
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.9
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 4,880
CDSs (total) :: 4,767
Genes (coding) :: 3,643
CDSs (with protein) :: 3,643
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) :: 1,124
CDSs (without protein) :: 1,124
Pseudo Genes (ambiguous residues) :: 0 of 1,124
Pseudo Genes (frameshifted) :: 378 of 1,124
Pseudo Genes (incomplete) :: 716 of 1,124
Pseudo Genes (internal stop) :: 255 of 1,124
Pseudo Genes (multiple problems) :: 201 of 1,124
##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"
/GO_function="GO:0003887 - DNA-directed DNA polymerase
activity [Evidence IEA]"
/GO_process="GO:0006270 - DNA replication initiation
[Evidence IEA]"
/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..2022
/locus_tag="SDY_RS24205"
CDS 1705..2022
/locus_tag="SDY_RS24205"
/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_001229902.1"
/translation="MALVSVTEAARLTGKNRAIIHRYIKQGKLSQISDATNTKKVDTS
ELIRVFGSLTATHATLSQSDAMQHDATPKTDQSVALLQQKIALLEQLLESKNNELQRQ
DER"
gene 2073..2770
/locus_tag="SDY_RS24210"
CDS join(2073..2322,2322..2770)
/locus_tag="SDY_RS24210"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_001743396.1"
/ribosomal_slippage
/GO_function="GO:0004803 - transposase activity [Evidence
IEA]"
/note="programmed frameshift; Derived by automated
computational analysis using gene prediction method:
Protein Homology."
/codon_start=1
/transl_table=11
/product="IS1 family transposase"
/protein_id="WP_238386298.1"
/translation="MASVSINCPSCSATDGGVRNGKSTAGHQRYLCSHCRKTWQLQFT
YTASQPGTHQKIIDMAMNGVGCRATARIMGVSLNTILRHFKKLRPQSVTSRIQPGSDV
IVCAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDV
VIWMTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELH
DKVIGHYLNIKHYQ"
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"
/EC_number="2.4.-.-"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_016247943.1"
/GO_function="GO:0016757 - glycosyltransferase activity
[Evidence IEA]"
/GO_process="GO:0006486 - protein glycosylation [Evidence
IEA]"
/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(4330..4920)
/locus_tag="SDY_RS24220"
/old_locus_tag="SDY_PA05"
CDS complement(4330..4920)
/locus_tag="SDY_RS24220"
/old_locus_tag="SDY_PA05"
/EC_number="2.4.-.-"
/inference="COORDINATES: protein motif:HMM:NF012745.6"
/GO_function="GO:0016757 - glycosyltransferase activity
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="glycosyltransferase family 2 protein"
/protein_id="WP_011898198.1"
/translation="MKNHKVSIIIPCFNNGKTIERCVLSALKQTHRNIEIICINDGPS
DNSWNILKKLSSLYGNVFAFNNEDNSGPSFSRIKGVSLSTGHFLSFLDADDYWHPKKL
ELQLSFINDENLDFLGSTCSIGEKNNQEINQGIKKEHLKLKIISFNMMLFKNYFQTPA
VIMKRDIFIPFNENQRFSEDYMSWLVIVYNKKTNVD"
gene complement(5080..5385)
/locus_tag="SDY_RS25320"
CDS complement(5080..5385)
/locus_tag="SDY_RS25320"
/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_000624216.1"
/translation="MISLAMSFVVMKNIPAVVTENNGASFVTEPNITERIVSKASDSD
RIARFKNAIVEISNLKTMFIGNGIGYSTLTQDPHNFYLSTIIDSSILILAIVMMVLY"
gene 6383..6907
/locus_tag="SDY_RS25325"
CDS 6383..6907
/locus_tag="SDY_RS25325"
/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_238386297.1"
/translation="MKKIVGRKYGKYISQISTDVFLAKITLSIIPIILALPLIYTTSS
GISIPNNWFVWLILFILSFGFTPFWYYISIENIIPPAILDLLLRVTGLILIVIFVNSP
SDAKTTIAIQSMVGALNTLISTAVVFYLSGVGAINIKRALNEIKDGFSVFLYKSSQGI
MITMSSSLLVFLGG"
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"
/GO_process="GO:0006313 - DNA transposition [Evidence
IEA]"
/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="IS1 family transposase"
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"
/GO_function="GO:0004803 - transposase activity [Evidence
IEA]"
/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)
//
