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Escherichia coli strain ECSC024 sequence77, whole genome shotgun sequence

NCBI Reference Sequence: NZ_BFHT01000077.1

FASTA Graphics 

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  JOURNAL   Unpublished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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