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Escherichia coli strain ARS-CC5560 NODE_108_length_2768_cov_33.9205_ID_13532, whole genome shotgun sequence

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  JOURNAL   Unpublished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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