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NCBI Reference Sequence: NZ_BGYR01000067.1
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LOCUS NZ_BGYR01000067 12204 bp DNA linear CON 04-SEP-2024 DEFINITION Escherichia coli strain TUM18764 sequence067, whole genome shotgun sequence. ACCESSION NZ_BGYR01000067 NZ_BGYR01000000 VERSION NZ_BGYR01000067.1 DBLINK BioProject: PRJNA224116 BioSample: SAMD00126589 Assembly: GCF_003306675.1 KEYWORDS WGS; RefSeq; STANDARD_DRAFT. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 AUTHORS Aoki,K. and Ishii,Y. TITLE A project of associating bacterial WGS and AST data JOURNAL Unpublished REFERENCE 2 (bases 1 to 12204) AUTHORS Aoki,K. and Ishii,Y. TITLE Direct Submission JOURNAL Submitted (28-JUN-2018) Contact:Kotaro Aoki Toho University; 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan COMMENT REFSEQ INFORMATION: The reference sequence is identical to BGYR01000067.1. 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 :: SPAdes v. 3.11 Genome Coverage :: 36.8x Sequencing Technology :: illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Name :: GCF_003306675.1-RS_2024_09_04 Annotation Date :: 09/04/2024 05:34:57 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) :: 5,689 CDSs (total) :: 5,565 Genes (coding) :: 5,273 CDSs (with protein) :: 5,273 Genes (RNA) :: 124 rRNAs :: 8, 5, 5 (5S, 16S, 23S) complete rRNAs :: 8, 1, 1 (5S, 16S, 23S) partial rRNAs :: 4, 4 (16S, 23S) tRNAs :: 95 ncRNAs :: 11 Pseudo Genes (total) :: 292 CDSs (without protein) :: 292 Pseudo Genes (ambiguous residues) :: 0 of 292 Pseudo Genes (frameshifted) :: 82 of 292 Pseudo Genes (incomplete) :: 230 of 292 Pseudo Genes (internal stop) :: 45 of 292 Pseudo Genes (multiple problems) :: 58 of 292 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..12204 /organism="Escherichia coli" /mol_type="genomic DNA" /submitter_seqid="sequence067" /strain="TUM18764" /host="Homo sapiens" /db_xref="taxon:562" /geo_loc_name="Japan" /collection_date="2017-03-31" /note="possess blaCTX-M-3" gene complement(<195..934) /locus_tag="DUP27_RS31305" /pseudo CDS complement(<195..934) /locus_tag="DUP27_RS31305" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_076612086.1" /note="frameshifted; 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="IS3 family transposase" misc_feature complement(537..653) /locus_tag="DUP27_RS31305" /inference="COORDINATES: nucleotide motif:Rfam:14.4:RF01497" /inference="COORDINATES: profile:INFERNAL:1.1.5" /note="AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch." /pseudo /db_xref="RFAM:RF01497" gene <987..1265 /locus_tag="DUP27_RS27980" /pseudo CDS <987..1265 /locus_tag="DUP27_RS27980" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000198547.1" /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="IS91 family transposase" gene complement(1788..2963) /gene="senB" /locus_tag="DUP27_RS27990" CDS complement(1788..2963) /gene="senB" /locus_tag="DUP27_RS27990" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001020413.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="enterotoxin production-related protein TieB" /protein_id="WP_001020413.1" /translation="MNIFTLSKAPLYLLISLFLPTMAMAIDPPERELSRFALKTNYLQ SPDEGVYELAFDNASKKVFAAVTDRVNREANKGYLYSFNSDSLKVENKYTMPYRAFSL AINQDKHQLYIGHTQSASLRISMFDTPTGKLVRTSDRLSFKAANAADSRFEHFRHMVY SQDSDTLFVSYSNMLKTAEGMKPLHKLLMLDGTTLALKGEVKDAYKGTAYGLTMDEKT QKIYVGGRDYINEIDAKNQTLLRTIPLKDPRPQITSVQNLAVDSASDRAFVVVFDHDD RSGTKDGLYIFDLRDGKQLGYVHTGAGANAVKYNPKYNELYVTNFTSGTISVVDATKY SITREFNMPVYPNQMVLSDDMDTLYIGIKEGFNRDWDPDVFVEGAKERILSIDLKKS" gene complement(3032..5293) /locus_tag="DUP27_RS27995" CDS complement(3032..5293) /locus_tag="DUP27_RS27995" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001100765.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="TonB-dependent receptor domain-containing protein" /protein_id="WP_001100763.1" /translation="MNVIKLAIGSGILLLSCGAYSQSISEKTNSDKKGAAEFSPLSVS VGKTTSEQEALEKTGATSSRTTDKNLQSLDATVRSMPGTYTQIDPGQGAISVNIRGMS GFGRVNTMVDGITQSFYGTSTSGTTTHGSTNNMAGVLIDPNLLVAVDVTRGDSSGSEG INALAGSANMRTIGVDDVIFNGNTYGLRSRFSVGSNGLGRSGMIALGGKSDAFTDTGS IGVMAAVSGSSVYSNFSNGSGINSKEFGYDKYMKQNPKSQLYKMDIRPDEFNSFELSA RTYENKFTRRDITSDDYYIKYHYTPFSELIDFNVTASTSRGNQKYRDGSLYTFYKTSA QNRSDALDINNTSRFTVADNDLEFMLGSKLMRTRYDRTIHSAAGDPKANQESIENNPF APSGQQDISALYTGLKVTRGIWEADFNLNYTRNRITGYKPACDSRVICVPQGSYDIDD KEGGFNPSVQLSAQVTPWLQPFIGYSKSMRAPNIQEMFFSNSGGASMNPFLKPERAET WQAGFNIDTRDLLVEQDALRFKALAYRSRIQNYIYSESYLVCSGGRKCSLPEVIGNGW EGISDEYSDNMYIYVNSASDVIAKGFELEMDYDAGFAFGRLSFSQQQTDQPTSIASTH FGAGDITELPRKYMTLDTGVRFFDNALTLGTIIKYTGKARRLSPDFEQDEHTGAIIKQ DLPQIPTIIDLYGTYEYNRNLTLKLSVQNLMNRDYSEALNKLNMMPGLGDETHPANSA RGRTWIFGGDIRF" gene complement(5462..6238) /locus_tag="DUP27_RS28000" CDS complement(5462..6238) /locus_tag="DUP27_RS28000" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000981087.1" /GO_component="GO:0016020 - membrane [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="energy transducer TonB" /protein_id="WP_000981091.1" /translation="MMNILHFSQSVKWSSWFICSLLLHGLIFLAFIWRFSEVQPAMSP APAIMLQWAEIIEAPSSPLSLPVGIAQQESAVTEEKQQTEDRQQRPVTEDSDATIEIT RKKKSSDGEKKKTRPPRKIKAQTSDSNPTAVSSNAAPQALVESSRIAAPFNSDSTKRD NSEASWESRVKGHLNRYKRYPGDARKRARTGTAVVTFTVNTEGTIVSSFLEISSGTFS LDREAIAVLERAQPLPKPPPEILEGGLFKVKMPITFKLKE" gene complement(6246..7121) /locus_tag="DUP27_RS28005" CDS complement(6246..7121) /locus_tag="DUP27_RS28005" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001224622.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="ChaN family lipoprotein" /protein_id="WP_001224623.1" /translation="MRKFILISMITLASVSLGACRQNVTIKQDAPGQKAFLTDGQIYD LHSGKIISSSELLADLATAQHLIIGEKHDNAEHHQIELWLIQNLLIQRPQGSVLLEML TSEQQPRVNQVKCWLKDNPVVRDSRVQELLNWQKGWSWEMYGDIVMQLLRGPYPLLNA NIGREQILALYKKNEFPKGKKSTAPVVQEALRETIISMHEGNLESQQLTSMLSIQQQR DRYMARQLLSAPVPSLLIAGGYHASKSMGVPLHMEDLATGTHPVVLMLAEKGMNITVD HADYVWFVAPDTTKR" gene complement(<7495..>8120) /locus_tag="DUP27_RS28010" /pseudo CDS complement(<7495..>8120) /locus_tag="DUP27_RS28010" /inference="COORDINATES: similar to AA sequence:RefSeq:YP_005221104.1" /note="frameshifted; 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="replication initiation protein" gene complement(9572..9907) /locus_tag="DUP27_RS28035" CDS complement(9572..9907) /locus_tag="DUP27_RS28035" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001080726.1" /GO_function="GO:0015643 - toxic substance binding [Evidence IEA]" /GO_process="GO:0030153 - bacteriocin immunity [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="colicin E1 family microcin immunity protein" /protein_id="WP_001080732.1" /translation="MNRKYYFNNMWWGWVTGGYMLYMSWDYDFKYRLLFWCISLCGMV LYPVAKWYIEDTALKFTRPDFWNSGFFTDTPGKMGLLAVYTGTVFILSLPLSMIYILS VIIKRLSVR" gene 10036..10383 /locus_tag="DUP27_RS28045" CDS 10036..10383 /locus_tag="DUP27_RS28045" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001563283.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="DUF6404 family protein" /protein_id="WP_000142452.1" /translation="MTFEQKKARAIALMDSKKMWRSNYAPPLLRILWRLGIRLPPLPF MPFWQVTVLTGGLWGISWGCAMWFIYWGPSGMVAGEAIIISITGGFLSGLLMASFHWW RRKVNRLPPWDDV" gene complement(10403..10912) /locus_tag="DUP27_RS28050" CDS complement(10403..10912) /locus_tag="DUP27_RS28050" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001545742.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="WP_000194542.1" /translation="MTQSRRPSPLQRRVLIVLAALDEKRPGPVLTRDIERVLEQSGEA PVYGPNLRASCRRLEDAGWLRTLRAPNLQLAVELTDAGRAVAQPLLPAGGTSATDLAV ELNGITYQACRGDFVVRLDGSTCLQLWNKEGRVVRREGDPLEVAQWLQACHDAGMEVR VQINESAAP" gene complement(10909..11169) /locus_tag="DUP27_RS28055" CDS complement(10909..11169) /locus_tag="DUP27_RS28055" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001523449.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="WP_000371882.1" /translation="MDQEMTFSLSYEQLTRFAEKRIRECNLDSHGVTYLCESAKAGAV LIFWHELAINGYTSMNAIKRQEIIDADHQRLRKLIWPEDDWK" gene 11271..>12010 /locus_tag="DUP27_RS31310" /pseudo CDS 11271..>12010 /locus_tag="DUP27_RS31310" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_076612086.1" /note="frameshifted; 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="IS3 family transposase" misc_feature 11552..11668 /locus_tag="DUP27_RS31310" /inference="COORDINATES: nucleotide motif:Rfam:14.4:RF01497" /inference="COORDINATES: profile:INFERNAL:1.1.5" /note="AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch." /pseudo /db_xref="RFAM:RF01497" CONTIG join(BGYR01000067.1:1..12204) //
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