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Escherichia coli strain TUM18764 sequence067, whole genome shotgun sequence

NCBI Reference Sequence: NZ_BGYR01000067.1

FASTA Graphics 

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  JOURNAL   Unpublished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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