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JOURNAL Unpublished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)
//