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NCBI Reference Sequence: NZ_SPVW01000188.1
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LOCUS NZ_SPVW01000188 6285 bp DNA linear CON 09-JUL-2024 DEFINITION Escherichia coli strain RUSPBB65 NODE_1103_length_6255_cov_30.690008, whole genome shotgun sequence. ACCESSION NZ_SPVW01000188 NZ_SPVW01000000 VERSION NZ_SPVW01000188.1 DBLINK BioProject: PRJNA224116 BioSample: SAMN11233093 Assembly: GCF_006229335.1 KEYWORDS WGS; RefSeq. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 6285) AUTHORS Naaber,P. TITLE Phenotypic and molecular epidemiology of Extended Spectrum Beta Lactamase producing Escherichia coli in Northern and Eastern Europe JOURNAL Unpublished REFERENCE 2 (bases 1 to 6285) AUTHORS Naaber,P. TITLE Direct Submission JOURNAL Submitted (27-MAR-2019) Bioinformatics, University of Tartu, Riia, Tartu 51010, Estonia COMMENT REFSEQ INFORMATION: The reference sequence is identical to SPVW01000188.1. 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 :: Velvet v. 1.2.10 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 67.58808828125x Sequencing Technology :: HiSeq2500 Rapid Run ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Name :: GCF_006229335.1-RS_2024_07_09 Annotation Date :: 07/09/2024 05:21:26 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) :: 5,315 CDSs (total) :: 5,228 Genes (coding) :: 4,865 CDSs (with protein) :: 4,865 Genes (RNA) :: 87 rRNAs :: 1, 3, 6 (5S, 16S, 23S) complete rRNAs :: 1 (5S) partial rRNAs :: 3, 6 (16S, 23S) tRNAs :: 65 ncRNAs :: 12 Pseudo Genes (total) :: 363 CDSs (without protein) :: 363 Pseudo Genes (ambiguous residues) :: 0 of 363 Pseudo Genes (frameshifted) :: 80 of 363 Pseudo Genes (incomplete) :: 301 of 363 Pseudo Genes (internal stop) :: 53 of 363 Pseudo Genes (multiple problems) :: 60 of 363 CRISPR Arrays :: 3 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..6285 /organism="Escherichia coli" /mol_type="genomic DNA" /submitter_seqid="NODE_1103_length_6255_cov_30.690008" /strain="RUSPBB65" /isolation_source="clinical sample" /host="Homo sapiens" /db_xref="taxon:562" /geo_loc_name="Russia" /collection_date="2012" /collected_by="Baltic ESBL Project" gene complement(<57..>636) /locus_tag="E3970_RS27655" /pseudo CDS complement(<57..>636) /locus_tag="E3970_RS27655" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000080195.1" /GO_function="GO:0004803 - transposase activity [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=2 /transl_table=11 /product="IS66 family transposase" gene complement(<647..>971) /locus_tag="E3970_RS27660" CDS complement(<647..>971) /locus_tag="E3970_RS27660" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_014839879.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=2 /transl_table=11 /product="IS66 family transposase zinc-finger binding domain-containing protein" /protein_id="WP_250383160.1" /translation="IEKLRRMLFGTRSEKLQREVEQAEAQLKQREQESDRYSGREDDP QVPRQLRQSRHRRPLPAHLPREIHRLEPEESCCPECGSELDYLGEVSAEQLELVSSAL KVIRTV" gene complement(<982..1170) /locus_tag="E3970_RS27665" /pseudo CDS complement(<982..1170) /locus_tag="E3970_RS27665" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000080164.1" /note="incomplete; too short partial abutting assembly gap; 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" gene complement(1201..>1326) /locus_tag="E3970_RS27670" /pseudo CDS complement(1201..>1326) /locus_tag="E3970_RS27670" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309365.1" /note="incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="IS66 family insertion sequence element accessory protein TnpB" gene complement(<1337..1507) /gene="tnpB" /locus_tag="E3970_RS27675" CDS complement(<1337..1507) /gene="tnpB" /locus_tag="E3970_RS27675" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309365.1" /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_139464947.1" /translation="MISLPSDTRISLVAGVTDMRKSFNGLGEQVQHVLDENPFSGHLF IFRGRRSDMIKIL" gene complement(1504..1929) /locus_tag="E3970_RS19025" CDS complement(1504..1929) /locus_tag="E3970_RS19025" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001373091.1" /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_000435655.1" /translation="MEQKILSAEPRRTFSNEFKLQMVKLASQLGASVARIAREHDIND NLLFKWLRLWQNEGRISRRLPVTTSSDAGVELLPVEITPDEQKEPMAALTPLLSTPSQ STVSASSCKVEFRHGNMTLENPSPELLTVLIRELTGRGR" gene complement(<2075..2473) /locus_tag="E3970_RS19030" /pseudo CDS complement(<2075..2473) /locus_tag="E3970_RS19030" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_005154742.1" /note="frameshifted; internal stop; 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="transposase domain-containing protein" gene 2591..>3507 /locus_tag="E3970_RS19035" CDS 2591..>3507 /locus_tag="E3970_RS19035" /EC_number="4.1.3.3" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001149830.1" /GO_function="GO:0008747 - N-acetylneuraminate lyase activity [Evidence IEA]" /GO_process="GO:0005975 - carbohydrate metabolic process [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="N-acetylneuraminate lyase" /protein_id="WP_001149834.1" /translation="MQCEFKGVISALPTPYDQSQQIDMESLRKLIRFNIEQNIKGLYV GGSTGEAFLQNVAEREKILETVADESDGRLTLIAHVGGISTAESEVLAKAAKKYGYHA ISAVTPFYYPFSFEEHCIHYRKIIDSADGLPMVVYNIPALSGVRFSLDQINELVTIPR VCALKQTSGDLFQMEQIKRNHPELVLYNGYDEIFASGLIAGADGGIGSTYNIMGWRYL EIFEAVKNNDVIKAKEMQVACNQVIDTLIQSGVLAGIKTLLYYMGIINTPVCRSPFSP VKEKNLDVLSKLAERLFEEHDRNKKMKII" gene 3521..>4032 /locus_tag="E3970_RS27680" CDS 3521..>4032 /locus_tag="E3970_RS27680" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000629094.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="ROK family protein" /protein_id="WP_252398950.1" /translation="MITLAVDIGGTKISAALISDDGSFLLKKQISTPHERCPDEMTGA LRLLVSEMKGTAERFAVASTGIINNGVLTALNPDNLGGLKEYPLKNIMEDITGLNGSV INDAQAAAWAEYTVLPKEICDMVFITVSTGVGGGIVVNRKLLTGVSGLAGHVGHILSG VTDTECGCGRR" gene <4047..4397 /locus_tag="E3970_RS27685" CDS <4047..4397 /locus_tag="E3970_RS27685" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000629094.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="ROK family protein" /protein_id="WP_250378629.1" /translation="AVSSGRAIMGAAKNKLAGYSTKYIFELARQGYKEAEFLTERSAS TIAELIVSLKLLLDCQVVVVGGSVGLADGYVQKVSKHLSIYSEICNVMLFPAYFRSDS GLIGATLWDRDCIT" gene 4446..5918 /locus_tag="E3970_RS19045" CDS 4446..5918 /locus_tag="E3970_RS19045" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000376547.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="MFS transporter" /protein_id="WP_000376547.1" /translation="MDSCIQKKQVWYKHLSPRQWKIFGAAWTGYLLDGFDFVLISLVL TEVQHEFGLTTIEAASLISAAFISRWFGGLAIGALSDKMGRRMAMVLSIVLFSLGTLA CGLAPGYAVMFIARIVIGLGMAGEYGSSVTYVIESWPVHLRNKASGFLISGFSIGGGL AAQVYSIVVPLWGWRSLFFVGMLPILFAFYLRKNLPESDDWQKRQQENKPVRTMVDIL YREKNKYINILLSCIAFACLYVCFSGVTANAALITVMALCCAAVFISFIYQGMGKRWP TGIMLMLVVMFCFLYGWPLQAFLPTWLKVDMQYSPETVALIFMLAGFGSAAGSCIGGF MGDWLGTRKAYVISLLIGQLVIIPVFLVDRDYVWLLGLLIFTQQVFGQGIGALVPKII SGYFNVEQRAAGLGFIYNVGSLGGACAPILGAVVASHTSLGTAMCSLAFILTFVVLVL IGFDMPSRVQRWIHPEAALEYDTVDGKPFYGARKKNVAEE" gene 5922..>6285 /locus_tag="E3970_RS19050" /pseudo CDS 5922..>6285 /locus_tag="E3970_RS19050" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000948499.1" /note="incomplete; too short partial abutting assembly gap; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="alpha/beta hydrolase" CONTIG join(SPVW01000188.1:1..6285) //
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