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NCBI Reference Sequence: NZ_UDWX01000104.1
FASTA Graphics
LOCUS NZ_UDWX01000104 12404 bp DNA linear CON 12-JUL-2024 DEFINITION Shigella flexneri strain 4028STDY6275015, whole genome shotgun sequence. ACCESSION NZ_UDWX01000104 NZ_UDWX01000000 VERSION NZ_UDWX01000104.1 DBLINK BioProject: PRJNA224116 BioSample: SAMEA3710457 Assembly: GCF_900486855.1 KEYWORDS WGS; RefSeq. SOURCE Shigella flexneri ORGANISM Shigella flexneri Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella. REFERENCE 1 AUTHORS Doyle,S. CONSRTM Pathogen Informatics TITLE Direct Submission JOURNAL Submitted (13-JUN-2018) WTSI, Pathogen Informatics, Wellcome Trust Sanger Institute, CB10 1SA, United Kingdom COMMENT REFSEQ INFORMATION: The reference sequence is identical to UDWX01000104.1. 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_900486855.1-RS_2024_07_12 Annotation Date :: 07/12/2024 01:42:31 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) :: 5,074 CDSs (total) :: 4,956 Genes (coding) :: 4,166 CDSs (with protein) :: 4,166 Genes (RNA) :: 118 rRNAs :: 8, 5, 1 (5S, 16S, 23S) complete rRNAs :: 3, 1 (5S, 23S) partial rRNAs :: 5, 5 (5S, 16S) tRNAs :: 97 ncRNAs :: 7 Pseudo Genes (total) :: 790 CDSs (without protein) :: 790 Pseudo Genes (ambiguous residues) :: 0 of 790 Pseudo Genes (frameshifted) :: 261 of 790 Pseudo Genes (incomplete) :: 484 of 790 Pseudo Genes (internal stop) :: 173 of 790 Pseudo Genes (multiple problems) :: 120 of 790 Pseudo Genes (short protein) :: 1 of 790 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..12404 /organism="Shigella flexneri" /mol_type="genomic DNA" /strain="4028STDY6275015" /serovar="2A" /db_xref="taxon:623" /note="contig: ERS1017606SCcontig000104" gene <1..127 /locus_tag="DTM52_RS18905" CDS <1..127 /locus_tag="DTM52_RS18905" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_076611998.1" /GO_process="GO:0015074 - DNA integration [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=2 /transl_table=11 /product="IS3 family transposase" /protein_id="WP_024185603.1" /translation="DEAISVIREYIEIFYNRQRRHSRLGNISPAAFREKYHQMAA" gene 139..543 /locus_tag="DTM52_RS18915" /old_locus_tag="SAMEA3710457_03753" CDS 139..543 /locus_tag="DTM52_RS18915" /old_locus_tag="SAMEA3710457_03753" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_011069416.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="WP_011069416.1" /translation="MVVSAIASTPQNTTLMSWDAVLYDLRSEKIISKDNYLTDLNRRH LELVLHTNPNPSGSVTKILRTIFTKQVKSLGPELCHFLHHELTKKRYEVWHHYDVLHY QSSSFSRSQFNALINLLAQQSRFADLKLSNYK" gene complement(631..1275) /gene="cheZ" /locus_tag="DTM52_RS18920" /old_locus_tag="SAMEA3710457_03754" CDS complement(631..1275) /gene="cheZ" /locus_tag="DTM52_RS18920" /old_locus_tag="SAMEA3710457_03754" /EC_number="3.6.1.-" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707776.2" /GO_function="GO:0003824 - catalytic activity [Evidence IEA]" /GO_process="GO:0050920 - regulation of chemotaxis [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="protein phosphatase CheZ" /protein_id="WP_000983598.1" /translation="MMQPSIKPADEHSAGDIIARIGSLTHMLRDSLRELGLVQAIAEA AEAIPDARDRLYYVVQMTAQAAERALNSVEASQPHQDQMEKSAKALTQRWDDWFADPI DLADARELVTDTRQFLADVPAHTSFTNAQLLEIMMAQDFQDLTGQVIKRMMDVIQEIE RQLLMVLLENIPEQESRPKRENQSLLNGPQVDTSKAGVVASQDQVDDLLDSLGF" gene complement(1286..1675) /gene="cheY" /locus_tag="DTM52_RS18925" /old_locus_tag="SAMEA3710457_03755" CDS complement(1286..1675) /gene="cheY" /locus_tag="DTM52_RS18925" /old_locus_tag="SAMEA3710457_03755" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_002210873.1" /GO_process="GO:0000160 - phosphorelay signal transduction system [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="chemotaxis response regulator CheY" /protein_id="WP_000763867.1" /translation="MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALN KLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAG ASGYVVKPFTAATLEEKLNKIFEKLGM" gene complement(1690..2739) /gene="cheB" /locus_tag="DTM52_RS18930" /old_locus_tag="SAMEA3710457_03756" CDS complement(1690..2739) /gene="cheB" /locus_tag="DTM52_RS18930" /old_locus_tag="SAMEA3710457_03756" /EC_number="3.1.1.61" /EC_number="3.5.1.44" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000036372.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="protein-glutamate methylesterase/protein glutamine deamidase" /protein_id="WP_000036372.1" /translation="MSKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDL IKKFNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLRALELGAI DFVTKPQLGIREGMLAYSEMIAEKVRTAAKASLAAHKPLSAPTTLKAGPLLSSEKLIA IGASTGGTEAIRHVLQPLPLSSPALLITQHMPPGFTRSFADRLNKLCQIGVKEAEDGE RVLPGHAYIAPGDRHMELARSGANYQIKIHDGPAVNRHRPSVDVLFHSVAKQAGRNAV GVILTGMGNDGAAGMLAMRQAGAWTLAQNEASCVVFGMPREAINMGGVCEVVDLSQVS QQMLATISAGQAIRI" gene complement(2742..3602) /gene="cheR" /locus_tag="DTM52_RS18935" /old_locus_tag="SAMEA3710457_03757" CDS complement(2742..3602) /gene="cheR" /locus_tag="DTM52_RS18935" /old_locus_tag="SAMEA3710457_03757" /EC_number="2.1.1.80" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707779.1" /GO_function="GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="protein-glutamate O-methyltransferase CheR" /protein_id="WP_000204331.1" /translation="MTSSLPCGQTSLLLQMTERLALSDAHFRRISQLIYQRAGIVLAD HKRDMVYNRLVRRLRSLGLTDFGHYLNLLESNQHSGEWQAFINSLTTNLTAFFREAHH FPLLADHARRRSGEDRVWSAAASTGEEPYSIAMTLADTLGTVPGRWKVFASDIDTEVL EKARSGIYRHEELKNLTPQQLQRYFMRGTGPHEGLVRVRQELANYVDFAPLNLLAKQY TVPGPFDAIFCRNVMIYFDQTTQQEILRRFVPLLKPDGLLFAGHSENFSHLERRFTLR GQTVYALSKD" gene complement(3621..5222) /gene="tap" /locus_tag="DTM52_RS18940" /old_locus_tag="SAMEA3710457_03758" CDS complement(3621..5222) /gene="tap" /locus_tag="DTM52_RS18940" /old_locus_tag="SAMEA3710457_03758" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707780.2" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="methyl-accepting chemotaxis protein IV" /protein_id="WP_000483183.1" /translation="MFNRIRISTTLFLILILCGILQIGSNGMSFWAFRDDLQRLNHGE QSNQQRAALAQTRAVMLQASTALNKAGTLTALSYPADDIKTLMTTARASLTQSTTLFK SFMAMTAGNEHVRALQKETEKSFARWHNDLEHQATWLESNQLSDFLTAPVQGSQNAFD VNFEAWQLEINHVLEAASAQSQRNYQISALVFISMIIVAAIYISSALWWTRKMIVQPL AIIGSHFDSIAAGNLARPIAVYGRNEITAIFASLKTMQQALRGTVSDVRKGSHEMHIG IAEIVAGNNDLSSRTEQQAASLAQTAASMEQLTATVGQNADNARQASELAKNAATTAQ AGGVQVSTMTHTMQEIATSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGF AVVAGEVRNLASRSAQAAKEIKGLIEESVNRVQQGSKLVNNAAATMTDIVSSVTRVND IMGEIASASEEQRRGIEQVAQAVSQMDQVTQQNSSLVEEAAVATEQLANQADHLSSRV AVFTLEEHEVARHESAQLQIAPVVS" gene complement(5268..6929) /gene="tar" /locus_tag="DTM52_RS18945" /old_locus_tag="SAMEA3710457_03759" CDS complement(5268..6929) /gene="tar" /locus_tag="DTM52_RS18945" /old_locus_tag="SAMEA3710457_03759" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707781.2" /GO_component="GO:0016020 - membrane [Evidence IEA]" /GO_function="GO:0004888 - transmembrane signaling receptor activity [Evidence IEA]" /GO_process="GO:0006935 - chemotaxis [Evidence IEA]; GO:0007165 - signal transduction [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="methyl-accepting chemotaxis protein II" /protein_id="WP_000610392.1" /translation="MINRIRVVTLLVMVLGVFALLQLISGSLFFSSLHHSQKSFVVSN QLREQQGELTSTWDLMLQTRINLSRSAVRMMMDSSNQQSNAKVELLDSARKTLAQAAT HYKKFKSMAPLPEMVATSRNFDEKYKNYYTALTELIDYLDYGNTGAYFAQPTQGMQNA MGEAFAQYALSSEKLYRDIVTDNADDYRFAQWQLAVIALVVVLILLVAWYGIRRMLLT PLAKIIAHICEIAGGNLANTLTIDGRSEMGDLAQSVSHMQRSLTDTVTHVREGSDAIY AGTREIAAGNTDLSSRTEQQASALEETAASMEQLTATVKQNADNARQASQLAQSASDT AQHGGKVVDGVVKTMHEIADSSKKIADIISVIDGIAFQTNILALNAAVEAARAGEQGR GFAVVAGEVRNLASRSALAAKEIKALIEDSVSRIDTGSVLVESAGETMNNIVNAVTRV TDIMGEIASASDEQSRGIDQVALAVSEMDRVTQQNASLVQESAAAAAALEEQASRLTQ AVSAFRLAASPLTNKPQTPSRPASEQPPAQPRLRITEQDPNWETF" gene complement(7074..7577) /gene="cheW" /locus_tag="DTM52_RS18950" /old_locus_tag="SAMEA3710457_03761" CDS complement(7074..7577) /gene="cheW" /locus_tag="DTM52_RS18950" /old_locus_tag="SAMEA3710457_03761" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_310624.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="chemotaxis protein CheW" /protein_id="WP_000147302.1" /translation="MTGMTNVTKLASEPSGQEFLVFTLGDEEYGIDILKVQEIRGYDQ VTRIANTPAFIKGVTNLRGVIVPIVDLRIKFSQVDVDYNDNTVVIVLNLGQRVVGIVV DGVSDVLSLTAEQIRPAPEFAVTLSTEYLTGLGALGDRMLILVNIEKLLNSEEMALLD SAASEVA" gene complement(7598..9562) /gene="cheA" /locus_tag="DTM52_RS18955" /old_locus_tag="SAMEA3710457_03762" CDS complement(7598..9562) /gene="cheA" /locus_tag="DTM52_RS18955" /old_locus_tag="SAMEA3710457_03762" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707783.2" /GO_function="GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]" /GO_process="GO:0006935 - chemotaxis [Evidence IEA]; GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="chemotaxis protein CheA" /protein_id="WP_000020706.1" /translation="MSIDISDFYQTFFDEADELLADMEQHLLVLQPEAPDAEQLNAIF RAAHSIKGGAGTFGFSVLQETTHLMENLLDEARRGEMQLNTDIINLFLETKDIMQEQL DAYKQSQEPDAASYDYICQALRQLALEAKGETPSAVTRLSVVAKSEPQDEQSRSQLPR RIILSRLKAGEVDLLEEELGHLTTLNDVVKGADSLSAILPGDIAEDDITAVLCFVIEA DQITFETVEVSPKIATPPVLKLAAEQAPTGRVEREKTTRSSESTSIRVAVEKVDQLIN LVGELVITQSMLAQRSSELDPVNHGDLITSMGQLQRNARDLQESVMSIRMMPMEYVFS RYPRLVRDLAGKLGKQVELTLVGSSTELDKSLIERIIDPLTHLVRNSLDHGIELPEKR LAAGKNSVGNLILSAEHQGGNICIEVTDDGAGLNRERILAKAASQGLTVSENMSDDEV AMLIFAPGFSTAEQVTDVSGRGVGMDVVKRNIQEMGGHVEIQSKQGTGTTIRILLPLT LAILDGMSVRVADEVFILPLNAVMESLQPREADLHPLAGGERVLEVRGEYLPIVELWK VFNVAGAKTEATQGIVVILQSGGRRYALLVDQLIGQHQVVVKNLESNYRKVPGISAAT ILGDGSVALIVDVSALQAINREQRMANTAA" gene complement(9567..10493) /gene="motB" /locus_tag="DTM52_RS18960" /old_locus_tag="SAMEA3710457_03763" CDS complement(9567..10493) /gene="motB" /locus_tag="DTM52_RS18960" /old_locus_tag="SAMEA3710457_03763" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707784.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="flagellar motor protein MotB" /protein_id="WP_000795618.1" /translation="MKNQAHPIIVVKRRKAKSHGAAHGSWKIAYADFMTAMMAFFLVM WLISISSPKELIQIAEYFRTPLATAVTGGDRISNSESPIPGGGDDYTQSQGEVNKQPN IEELKKRMEQSRLRKLRGDLDQLIESDPKLRALRLHLKIDLVQEGLRIQIIDSQNRPM FRTGSADVEPYMRDILRAIAPVLNGIPNRISLSGHTDDFPYASGEKGYSNWELSADRA NASRRELMVGGLDSGKVLRVVGMAATMRLSDRGPDDAVNRRISLLVLNKQAEQAILHE NAESQNEPVSALEKPEVAPQVSVPTMPSAEPR" gene complement(10490..11377) /gene="motA" /locus_tag="DTM52_RS18965" /old_locus_tag="SAMEA3710457_03764" CDS complement(10490..11377) /gene="motA" /locus_tag="DTM52_RS18965" /old_locus_tag="SAMEA3710457_03764" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_707785.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="flagellar motor stator protein MotA" /protein_id="WP_000906331.1" /translation="MLILLGYLVVLGTVFGGYLMTGGSLGALYQPAELVIIAGAGIGS FIVGNNGKAIKGTLKALPLLFRRSKYTKAMYMDLLALLYRLMAKSRQMGMFSLERDIE NPRESEIFASYPRILADSVMLDFIVDYLRLIISGHMNTFEIEALMDEEIETHESEAEV PANSLALVGDSLPAFGIVAAVMGGVHALGSADRPAAELGALIAHAMVGTFLGILLAYG FISPLASVLRQKSAETSKMMQCVKVTLLSNLNGYAPPIAVEFGRKTLYSSERPSFIEL EEHVRAVKNPQQQTTTEEA" gene complement(11504..12082) /gene="flhC" /locus_tag="DTM52_RS18970" /old_locus_tag="SAMEA3710457_03765" CDS complement(11504..12082) /gene="flhC" /locus_tag="DTM52_RS18970" /old_locus_tag="SAMEA3710457_03765" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_310628.1" /GO_function="GO:0003677 - DNA binding [Evidence IEA]" /GO_process="GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="flagellar transcriptional regulator FlhC" /protein_id="WP_001291603.1" /translation="MSEKSIVQEARDIQLAMELITLGARLQMLESETQLSRGRLIKLY KELRGSPPPKGMLPFSTDWFMTWEQNVHASMFCNAWQFLLKTGLCNGVDAVIKAYRLY LEQCPQAEEGPLLALTRAWTLVRFVESGLLQLSSCNCCGGNFITHAHQPVGSFACSLC QPPSRAVKRRKLSQNPADIIPQLLDEQRVQAV" gene complement(12085..>12303) /locus_tag="DTM52_RS18975" /old_locus_tag="SAMEA3710457_03766" /pseudo CDS complement(12085..>12303) /locus_tag="DTM52_RS18975" /old_locus_tag="SAMEA3710457_03766" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_416406.4" /GO_process="GO:0044780 - bacterial-type flagellum assembly [Evidence IEA]; GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]" /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="flagellar transcriptional regulator FlhD" gene 12345..>12404 /locus_tag="DTM52_RS27420" CDS 12345..>12404 /locus_tag="DTM52_RS27420" /inference="COORDINATES: protein motif:HMM:NF015750.4" /GO_process="GO:0006313 - DNA transposition [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="IS1 family transposase" /protein_id="WP_130054469.1" /translation="MASISIRCPSCSATEGVVRN" CONTIG join(UDWX01000104.1:1..12404) //
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