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)
//
