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NCBI Reference Sequence: NZ_NFRA01000108.1
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LOCUS NZ_NFRA01000108 2768 bp DNA linear CON 14-JUN-2024 DEFINITION Escherichia coli strain ARS-CC5560 NODE_108_length_2768_cov_33.9205_ID_13532, whole genome shotgun sequence. ACCESSION NZ_NFRA01000108 NZ_NFRA01000000 VERSION NZ_NFRA01000108.1 DBLINK BioProject: PRJNA224116 BioSample: SAMN06855910 Assembly: GCF_002164025.1 KEYWORDS WGS; RefSeq. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 2768) AUTHORS Kim,S.-W., Karns,J.S., Van Kessel,J.A.S. and Haley,B.J. TITLE Genome Sequences of Thirty Escherichia coli O157:H7 Isolates Recovered from a Single Dairy Farm and its Associated Off-Site Heifer Raising Facility JOURNAL Unpublished REFERENCE 2 (bases 1 to 2768) AUTHORS Kim,S.-W. TITLE Direct Submission JOURNAL Submitted (15-MAY-2017) ARS, USDA, 10300 Baltimore Avenue, Beltsville, MD 20705, USA COMMENT REFSEQ INFORMATION: The reference sequence is identical to NFRA01000108.1. 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 Date :: 01-MAR-2016 Assembly Method :: SPAdes v. 3.7.0 Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 101x Sequencing Technology :: Illumina NextSeq 500 ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Name :: GCF_002164025.1-RS_2024_06_14 Annotation Date :: 06/14/2024 01:44:14 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) :: 5,431 CDSs (total) :: 5,335 Genes (coding) :: 4,964 CDSs (with protein) :: 4,964 Genes (RNA) :: 96 rRNAs :: 2, 2, 1 (5S, 16S, 23S) complete rRNAs :: 2, 1, 1 (5S, 16S, 23S) partial rRNAs :: 1 (16S) tRNAs :: 83 ncRNAs :: 8 Pseudo Genes (total) :: 371 CDSs (without protein) :: 371 Pseudo Genes (ambiguous residues) :: 0 of 371 Pseudo Genes (frameshifted) :: 108 of 371 Pseudo Genes (incomplete) :: 251 of 371 Pseudo Genes (internal stop) :: 70 of 371 Pseudo Genes (multiple problems) :: 47 of 371 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..2768 /organism="Escherichia coli" /mol_type="genomic DNA" /submitter_seqid="NODE_108_length_2768_cov_33.9205_ID_1353 2" /strain="ARS-CC5560" /isolation_source="fecal grab" /host="bovine" /db_xref="taxon:562" /geo_loc_name="USA: Pennsylvania" /collection_date="2010-06-30" /collected_by="Jo Ann Van Kessel" gene complement(<73..369) /locus_tag="CAC24_RS27025" /pseudo CDS complement(<73..369) /locus_tag="CAC24_RS27025" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309636.1" /GO_function="GO:0003677 - DNA binding [Evidence IEA]; GO:0008907 - integrase activity [Evidence IEA]" /GO_process="GO:0015074 - DNA integration [Evidence IEA]" /note="incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="phage integrase Arm DNA-binding domain-containing protein" gene complement(359..595) /locus_tag="CAC24_RS27030" CDS complement(359..595) /locus_tag="CAC24_RS27030" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309637.1" /GO_function="GO:0003677 - DNA binding [Evidence IEA]" /GO_process="GO:0006310 - DNA recombination [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="excisionase" /protein_id="WP_000088655.1" /translation="MSRLITLRDWAKEEFGDLAPSERVLKKYAQGKMMAPPAIKVGRY WMIDRNSRFVGTLAEPQLPINANPKLQRIIADGC" gene <735..1523 /locus_tag="CAC24_RS27035" /pseudo CDS <735..1523 /locus_tag="CAC24_RS27035" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_016247981.1" /note="incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="replication protein" gene 1520..2221 /locus_tag="CAC24_RS27040" CDS 1520..2221 /locus_tag="CAC24_RS27040" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309639.1" /GO_process="GO:0006270 - DNA replication initiation [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="replication protein P" /protein_id="WP_000788869.1" /translation="MKNIAAQMVNFDREQMRRIANNMPEQYDEKPQVQQVAQIINGVF SQLLATFPASLANRDQNELNEIRRQWVLAFRENGITTMEQVNAGMRVARRQNRPFLPS PGQFVAWCREEASVIAGLPNVSELVDMVYEYCRKRGLYPDAESYPWKSNAHYWLVTNL YQNMRANALTDAELRRKAADELTCMTARINRGETIPEPVKQLPVMGGRPLNRAQALAK IAEIKAKFGLKGASV" gene 2218..2520 /locus_tag="CAC24_RS27045" CDS 2218..2520 /locus_tag="CAC24_RS27045" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309640.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="protein ren" /protein_id="WP_000145915.1" /translation="MTGKEAIIHYLGTHKSFCAQDVAAVTGATVTSINQAAAKMARAG ILVVDGKVWRTVYYRFATREEREGKVSTNLIFKECRQSAAMKRVLRVYKRTSMGTQ" gene 2588..>2768 /locus_tag="CAC24_RS27050" CDS 2588..>2768 /locus_tag="CAC24_RS27050" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_309641.1" /GO_component="GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]" /GO_function="GO:0022857 - transmembrane transporter activity [Evidence IEA]" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="SMR family transporter" /protein_id="WP_072115438.1" /translation="MNPYIYLGGAILAEVIGTTLMKFSEGFTRLWPSVGTIICYCASF WLLAQTLAYIPTGIAY" CONTIG join(NFRA01000108.1:1..2768) //
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