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Escherichia coli UMEA 3041-1 acYyc-supercont1.7, whole genome shotgun sequence

NCBI Reference Sequence: NZ_KE701463.1

FASTA Graphics 

LOCUS       NZ_KE701463             1638 bp    DNA     linear   CON 09-JUN-2024
DEFINITION  Escherichia coli UMEA 3041-1 acYyc-supercont1.7, whole genome
            shotgun sequence.
ACCESSION   NZ_KE701463 NZ_AWAW01000000
VERSION     NZ_KE701463.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN01885888
            Assembly: GCF_000460015.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli UMEA 3041-1
  ORGANISM  Escherichia coli UMEA 3041-1
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1638)
  AUTHORS   Feldgarden,M., Frimodt-Moller,N., Leihof,R.F., Rasmussen,L.,
            Young,S.K., Zeng,Q., Gargeya,S., Abouelleil,A., Alvarado,L.,
            Berlin,A.M., Chapman,S.B., Gainer-Dewar,J., Goldberg,J., Gnerre,S.,
            Griggs,A., Gujja,S., Hansen,M., Howarth,C., Imamovic,A.,
            Larimer,J., McCowan,C., Murphy,C., Pearson,M., Poon,T., Priest,M.,
            Roberts,A., Saif,S., Shea,T., Sykes,S., Wortman,J., Nusbaum,C. and
            Birren,B.
  CONSRTM   The Broad Institute Genome Sequencing Platform, The Broad Institute
            Genome Sequencing Center for Infectious Disease
  TITLE     The Genome Sequence of Escherichia coli UMEA 3041-1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1638)
  AUTHORS   Feldgarden,M., Frimodt-Moller,N., Leihof,R.F., Rasmussen,L.,
            Young,S.K., Zeng,Q., Gargeya,S., Abouelleil,A., Alvarado,L.,
            Berlin,A.M., Chapman,S.B., Gainer-Dewar,J., Goldberg,J., Gnerre,S.,
            Griggs,A., Gujja,S., Hansen,M., Howarth,C., Imamovic,A.,
            Larimer,J., McCowan,C., Murphy,C., Pearson,M., Poon,T., Priest,M.,
            Roberts,A., Saif,S., Shea,T., Sykes,S., Wortman,J., Nusbaum,C. and
            Birren,B.
  CONSRTM   The Broad Institute Genome Sequencing Platform, The Broad Institute
            Genome Sequencing Center for Infectious Disease
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JUL-2013) Broad Institute of MIT and Harvard, 7
            Cambridge Center, Cambridge, MA 02142, USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            KE701463.1.
            Please be aware that the annotation is done automatically with
            little or no manual curation.
            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       :: allpaths v. R46484
            Assembly Name         :: Esch_coli_UMEA_3041-1_V1
            Genome Coverage       :: 145.0x
            Sequencing Technology :: Illumina
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000460015.1-RS_2024_06_09
            Annotation Date                   :: 06/09/2024 02:13:48
            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)                     :: 5,172
            CDSs (total)                      :: 5,082
            Genes (coding)                    :: 4,858
            CDSs (with protein)               :: 4,858
            Genes (RNA)                       :: 90
            rRNAs                             :: 4, 3, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 4, 2, 4 (5S, 16S, 23S)
            partial rRNAs                     :: 1 (16S)
            tRNAs                             :: 73
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 69 of 224
            Pseudo Genes (incomplete)         :: 157 of 224
            Pseudo Genes (internal stop)      :: 48 of 224
            Pseudo Genes (multiple problems)  :: 45 of 224
            Pseudo Genes (short protein)      :: 1 of 224
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..1638
                     /organism="Escherichia coli UMEA 3041-1"
                     /mol_type="genomic DNA"
                     /submitter_seqid="acYyc-supercont1.7"
                     /strain="UMEA 3041-1"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1281176"
                     /geo_loc_name="Sweden"
                     /collection_date="1996"
     gene            complement(388..525)
                     /locus_tag="G901_RS28775"
     CDS             complement(388..525)
                     /locus_tag="G901_RS28775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISV
                     Q"
     gene            573..914
                     /locus_tag="G901_RS0126460"
     CDS             573..914
                     /locus_tag="G901_RS0126460"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /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_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIV
                     ISTILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFG
                     LLGLFISIKNN"
     gene            complement(911..>1638)
                     /locus_tag="G901_RS00045"
                     /old_locus_tag="G901_05037"
     CDS             complement(911..>1638)
                     /locus_tag="G901_RS00045"
                     /old_locus_tag="G901_05037"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447003.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_021553234.1"
                     /translation="DEMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSR
                     IHDAEDNLKTAQTNLLNSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKI
                     SNVNEALAAFEKYKDVLNKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHV
                     SFGYDVVSDILKIKDTGDWKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAI
                     VTGILCAFIDKNKLNTINEVLGI"
CONTIG      join(AWAW01000053.1:1..1638)
//
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