LOCUS NZ_NJZS01000100 4890 bp DNA linear CON 26-APR-2024
DEFINITION Escherichia coli strain MOD1-EC1543
MOD1-EC1543_100_length_4890_cov_22.1762, whole genome shotgun
sequence.
ACCESSION NZ_NJZS01000100 NZ_NJZS01000000
VERSION NZ_NJZS01000100.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN05591721
Assembly: GCF_002461955.1
KEYWORDS WGS; RefSeq.
SOURCE Escherichia coli
ORGANISM Escherichia coli
Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE 1 (bases 1 to 4890)
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 4890)
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
NJZS01000100.1.
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 :: 21.8x
Sequencing Technology :: Illumina NextSeq 500
##Genome-Assembly-Data-END##
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Name :: GCF_002461955.1-RS_2024_04_26
Annotation Date :: 04/26/2024 02:40:19
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) :: 5,366
CDSs (total) :: 5,273
Genes (coding) :: 4,934
CDSs (with protein) :: 4,934
Genes (RNA) :: 93
rRNAs :: 7, 4, 1 (5S, 16S, 23S)
complete rRNAs :: 7, 1 (5S, 23S)
partial rRNAs :: 4 (16S)
tRNAs :: 71
ncRNAs :: 10
Pseudo Genes (total) :: 339
CDSs (without protein) :: 339
Pseudo Genes (ambiguous residues) :: 0 of 339
Pseudo Genes (frameshifted) :: 110 of 339
Pseudo Genes (incomplete) :: 247 of 339
Pseudo Genes (internal stop) :: 57 of 339
Pseudo Genes (multiple problems) :: 65 of 339
Pseudo Genes (short protein) :: 3 of 339
CRISPR Arrays :: 2
##Genome-Annotation-Data-END##
FEATURES Location/Qualifiers
source 1..4890
/organism="Escherichia coli"
/mol_type="genomic DNA"
/submitter_seqid="MOD1-EC1543_100_length_4890_cov_22.1762"
/strain="MOD1-EC1543"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:562"
/geo_loc_name="Guinea-Bissau"
/collection_date="1997"
/collected_by="Michigan State University"
gene <1..3216
/locus_tag="BF020_RS26695"
CDS <1..3216
/locus_tag="BF020_RS26695"
/inference="COORDINATES: similar to AA
sequence:RefSeq:NP_415890.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="phage tail protein"
/protein_id="WP_096858468.1"
/translation="SMDVEHGQYSVTLLVEGFPPSHAGTITVYEGSRSGTLNDFLGAM
TEDDVRPEALRRFEQMVEEVSRNASAVAQNTAAAKKSASDASASASEAATHATDAAAS
ARAASTSAGQAASSAQSASSSAGTASTKTREAAKSAAAAESSKSAAATSASAAKTSET
NAAASQKSAATSASTATTKASEAATSARGAATSKEAAKSSETNASSSASSAASSATAA
GNSAKAAKTSETNAKSSETAAGQSASAAAGSKTAAALSASAASTSAGQASASATAAGK
SAESAASSASTATTKAGEATEQASAAARSASAAKTSETNAKASETSAESSKTAAASSA
SSAASSASSASASKDEATRQASAAKGSATTASTKATEAAGSATAAAQSKSTAESAATR
AETAAKRAEDIASAVALEDASTTKKGIVQLSSATNSTSETLAATPKAVKSAYDNAEKR
LQKDQNGADIPDKGRFLNNINAVSKTDFADKRGMRYVRVNAPAGATSGKYYPVVVMRS
AGSVSELASRVIITTATRTAGDPMNNCEFNGFVMPGGWTDRGRYAYGMFWQYQNNERA
IHSIMMSNKGDDLRSVFYVDGAAFPVFAFIEDGLSISAPGADLVVNDTTYKFGATNPA
TECIAADVILDFKSGRGFYESHSLIVNDNLSCKKLFATDEIVARGGNQIRMIGGEYGA
LWRNDGAKTYLLLTNQGDVYGGWNTLRPFAIDNATGELVIGTKLSASLNGNALTATKL
QTPRRVSGVEFDGSKDITLTAAHVAAFARRATDTYADADGGVPWNAESGAYNVTRSGD
SYILVNFYTGVGSCRTLQMKAHYRNGGLFYRSSRDGYGFEEDWAEVYTSKNLPPESYP
VGAPIPWPSDTVPSGYALMQGQTFDKSAYPKLAAAYPSGVIPDMRGWTIKGKPASGRA
VLSQEQDGIKSHTHSASASSTDLGTKTTSSFDYGTKSTNNTGAHTHSVSGSTNSAGAH
THSLANVNTASANSGAGSASTRLSVVHNQNYATSSAGAHTHSLSGTAASAGAHAHTVG
IGAHTHSVAIGSHGHTITVNAAGNAENTVKNIAFNYIVRLA"
gene 3216..3800
/locus_tag="BF020_RS26700"
CDS 3216..3800
/locus_tag="BF020_RS26700"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_000885598.1"
/GO_process="GO:0098004 - virus tail fiber assembly
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="tail fiber assembly protein"
/protein_id="WP_001460683.1"
/translation="MAFRMSEQPRTIKIYNLLAGTNEFIGEGDAYIPPHTGLPANSTD
IAPPDIPAGFVAVFNSDEASWHLVEDHRGKTVYDVASGDALFISELGSLPENVTWLSP
EGEYQKWNSTAWVKDTEAEKLFRIREAEETKNSLMQVASEHIAPLQDAVDLEIATEEE
TSLLEAWKKYRVLLNRVNTTTAPDIEWPTVPIIE"
gene complement(3874..>4890)
/locus_tag="BF020_RS26705"
CDS complement(3874..>4890)
/locus_tag="BF020_RS26705"
/EC_number="2.7.7.65"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_000586336.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="GGDEF domain-containing protein"
/protein_id="WP_096858469.1"
/translation="IYQKSNDIAIYYLFRQFSFISIIFLAIYSTNVKNKSVLEDKRNI
IIVVLSILILFITPFVAKNLSSDNIKYSLNIIQYSLNRHLPTWNIVYTKIISVFWLVL
LISSCISIRNYSKIWLCIILISIVSVCNNLILLYFIDKSHPAWYMTKFLELISMIYII
STLMYYVFRKLNHANHMAIHDPLTNTYNRRYFIDSLKNISKHHDFSVIMLDIDSFKSI
NDKWGHHMGDQVIVMVTRIIKKSIRKEDILGRLGGEEFGIIIKGNTQKLLLSIAERIR
KNIEEQCSEKLLSHGPEKITVSIGCFTSKENNLSPSEMLVNADKALYQAKRTGKNKVI
IHSK"
CONTIG join(NJZS01000100.1:1..4890)
//