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NCBI Reference Sequence: NZ_BFHT01000077.1
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LOCUS NZ_BFHT01000077 3242 bp DNA linear CON 23-AUG-2024 DEFINITION Escherichia coli strain ECSC024 sequence77, whole genome shotgun sequence. ACCESSION NZ_BFHT01000077 NZ_BFHT01000000 VERSION NZ_BFHT01000077.1 DBLINK BioProject: PRJNA224116 BioSample: SAMD00076998 Sequence Read Archive: DRR102590 Assembly: GCF_005382525.1 KEYWORDS WGS; RefSeq; STANDARD_DRAFT. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 AUTHORS Arimizu,Y. and Ogura,Y. TITLE Large scale genomics of bovine and human commensal E. coli to reveal the emerging process of EHEC JOURNAL Unpublished REFERENCE 2 (bases 1 to 3242) AUTHORS Arimizu,Y., Tanizawa,Y. and Ogura,Y. TITLE Direct Submission JOURNAL Submitted (24-APR-2018) Contact:Yoshitoshi Ogura Kyushu University, Department of Bacteriology, Faculty of Medical Sciences; 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan URL :http://www.bact.med.kyushu-u.ac.jp COMMENT REFSEQ INFORMATION: The reference sequence is identical to BFHT01000077.1. 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-Assembly-Data-START## Assembly Method :: Platanus v. 1.2.2 Genome Coverage :: 50x Sequencing Technology :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Name :: GCF_005382525.1-RS_2024_08_23 Annotation Date :: 08/23/2024 20:11:09 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision :: 6.8 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total) :: 5,128 CDSs (total) :: 5,018 Genes (coding) :: 4,787 CDSs (with protein) :: 4,787 Genes (RNA) :: 110 rRNAs :: 8, 6, 11 (5S, 16S, 23S) complete rRNAs :: 7 (5S) partial rRNAs :: 1, 6, 11 (5S, 16S, 23S) tRNAs :: 79 ncRNAs :: 6 Pseudo Genes (total) :: 231 CDSs (without protein) :: 231 Pseudo Genes (ambiguous residues) :: 0 of 231 Pseudo Genes (frameshifted) :: 92 of 231 Pseudo Genes (incomplete) :: 162 of 231 Pseudo Genes (internal stop) :: 34 of 231 Pseudo Genes (multiple problems) :: 51 of 231 Pseudo Genes (short protein) :: 1 of 231 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..3242 /organism="Escherichia coli" /mol_type="genomic DNA" /submitter_seqid="sequence77" /strain="ECSC024" /isolation_source="blood" /host="Homo sapiens" /db_xref="taxon:562" /geo_loc_name="Japan" /collection_date="2008" gene <1..1357 /gene="ltrA" /locus_tag="FE926_RS25725" /old_locus_tag="ExPECSC024_04869" CDS <1..1357 /gene="ltrA" /locus_tag="FE926_RS25725" /old_locus_tag="ExPECSC024_04869" /EC_number="2.7.7.49" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_708749.1" /GO_function="GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]" /GO_process="GO:0000373 - Group II intron splicing [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=2 /transl_table=11 /product="group II intron reverse transcriptase/maturase" /protein_id="WP_031935869.1" /translation="NKTMLQARLAVELQILRDELLSGHYQPLPARRVYIPKSNGKLRP LGIPALRDRIVQRAMLMAMEPIWESDFHTLSYGFRPERSVHHAIRTVKLQLTDCGETR GRWVIEGDLSSYFDTVHHRLLMKAVRRRISDARFMTLLWKTIKAGHIDVGLFRAASEG VPQGGVISPLLSNIMLNEFDQYLHERYLSGKARKDRWYWNNSIQRGRSTAVRENWQWK PAVAYCRYADDFVLIVKGTKAQAEAIREECRGVLEGSLKLRLNMDKTKITHVNDGFIF LGHRIIRKRSRYGEMRVVSTIPQEKARNFAASLTALLSGNYSESKVDMAEQLNRKLKG WAMFYQFVDFKAKVFSYIDRVVFWKLAHWLARKYRTGIASLMRWWCKSPKPGQSKTWV LFGKTNHGKLSGEILYWLVGQGKKLFRWRLPEGNPYLRTETRNTYTSRFTEVAMAFAS I" gene <1441..>1779 /locus_tag="FE926_RS25730" /old_locus_tag="ExPECSC024_04870" /pseudo CDS <1441..>1779 /locus_tag="FE926_RS25730" /old_locus_tag="ExPECSC024_04870" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_076612086.1" /GO_process="GO:0015074 - DNA integration [Evidence IEA]" /note="incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="DDE-type integrase/transposase/recombinase" gene 1859..2263 /locus_tag="FE926_RS25735" /old_locus_tag="ExPECSC024_04871" CDS 1859..2263 /locus_tag="FE926_RS25735" /old_locus_tag="ExPECSC024_04871" /inference="COORDINATES: protein motif:HMM:NF013677.5" /GO_function="GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]" /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="IS66-like element accessory protein TnpA" /protein_id="WP_000839179.1" /translation="MKSLTAVRKKSPNYPVEFKIKMVELSHRPEISVAQLAREHGIND NLLFKWRQYWREGKLRPPSTTENNVPELLPITLDAEDVVPTTSPRSQPVAAATPESLN ISCEVTFRHGSLRLNGAISENILNLLIRELKR" gene 2260..2607 /gene="tnpB" /locus_tag="FE926_RS25740" /old_locus_tag="ExPECSC024_04872" CDS 2260..2607 /gene="tnpB" /locus_tag="FE926_RS25740" /old_locus_tag="ExPECSC024_04872" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_311895.1" /note="TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="IS66 family insertion sequence element accessory protein TnpB" /protein_id="WP_000612626.1" /translation="MIPLPSGTKIWLVAGITDMRNGFNGLAAKVQTTLKDDPMSGHVF IFRGRNGSQVKLLWSTGDGLCLLTKRLERGRFAWPSARDGKVFLTPAQLAMLLEGIDW RQPKRLLTSLTML" gene 2656..>3242 /locus_tag="FE926_RS25745" /pseudo CDS 2656..>3242 /locus_tag="FE926_RS25745" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000099160.1" /note="frameshifted; incomplete; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="IS66 family transposase zinc-finger binding domain-containing protein" CONTIG join(BFHT01000077.1:1..3242) //
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