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Shigella flexneri strain 4028STDY6275015, whole genome shotgun sequence

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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