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Escherichia coli strain RUSPBB65 NODE_1103_length_6255_cov_30.690008, whole genome shotgun sequence

NCBI Reference Sequence: NZ_SPVW01000188.1

FASTA Graphics 

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  JOURNAL   Unpublished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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