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Escherichia coli strain MOD1-EC1666 MOD1-EC1666_107_length_4306_cov_63.1163, whole genome shotgun sequence

NCBI Reference Sequence: NZ_NJUP01000107.1

FASTA Graphics 

LOCUS       NZ_NJUP01000107         4306 bp    DNA     linear   CON 28-APR-2024
DEFINITION  Escherichia coli strain MOD1-EC1666
            MOD1-EC1666_107_length_4306_cov_63.1163, whole genome shotgun
            sequence.
ACCESSION   NZ_NJUP01000107 NZ_NJUP01000000
VERSION     NZ_NJUP01000107.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN05607377
            Assembly: GCF_002460615.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4306)
  AUTHORS   Gangiredla,J., Mammel,M.K., Barnaba,T.J., Tartera,C., Gebru,S.T.,
            Patel,I.R., Leonard,S.R., Kotewicz,M.L., Lampel,K.A., Elkins,C.A.
            and Lacher,D.W.
  TITLE     Species-Wide Collection of Escherichia coli Isolates for
            Examination of Genomic Diversity
  JOURNAL   Genome Announc 5 (50), e01321-17 (2017)
   PUBMED   29242221
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4306)
  AUTHORS   Gangiredla,J., Barnaba,T., Gebru,S., Mammel,M.K., Lacher,D.,
            Tartera,C., Patel,I.R., Leonard,S., Lampel,K.A. and Elkins,C.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUN-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            NJUP01000107.1.
            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. 3.8.2
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 57.6x
            Sequencing Technology  :: Illumina NextSeq 500
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002460615.1-RS_2024_04_28
            Annotation Date                   :: 04/28/2024 01:25:34
            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)                     :: 5,598
            CDSs (total)                      :: 5,509
            Genes (coding)                    :: 5,173
            CDSs (with protein)               :: 5,173
            Genes (RNA)                       :: 89
            rRNAs                             :: 3, 2, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1 (5S, 16S)
            partial rRNAs                     :: 2, 1, 2 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 336
            CDSs (without protein)            :: 336
            Pseudo Genes (ambiguous residues) :: 0 of 336
            Pseudo Genes (frameshifted)       :: 88 of 336
            Pseudo Genes (incomplete)         :: 231 of 336
            Pseudo Genes (internal stop)      :: 55 of 336
            Pseudo Genes (multiple problems)  :: 37 of 336
            Pseudo Genes (short protein)      :: 2 of 336
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..4306
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /submitter_seqid="MOD1-EC1666_107_length_4306_cov_63.1163"
                     /strain="MOD1-EC1666"
                     /serotype="O174:H8"
                     /isolation_source="feces (Ovis aries)"
                     /host="Ovis aries"
                     /db_xref="taxon:562"
                     /geo_loc_name="Norway"
                     /collection_date="2001"
                     /collected_by="Michigan State University"
     gene            <1..>4306
                     /gene="cdiA"
                     /locus_tag="BGJ64_RS27510"
                     /pseudo
     CDS             <1..>4306
                     /gene="cdiA"
                     /locus_tag="BGJ64_RS27510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001385946.1"
                     /note="incomplete; too short partial abutting assembly
                     gap; 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="contact-dependent inhibition toxin CdiA"
CONTIG      join(NJUP01000107.1:1..4306)
//
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