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Escherichia coli strain EC36291 36291_S17-contig_64, whole genome shotgun sequence

NCBI Reference Sequence: NZ_VTOT01000064.1

FASTA Graphics 

LOCUS       NZ_VTOT01000064         5978 bp    DNA     linear   CON 22-DEC-2024
DEFINITION  Escherichia coli strain EC36291 36291_S17-contig_64, whole genome
            shotgun sequence.
ACCESSION   NZ_VTOT01000064 NZ_VTOT01000000
VERSION     NZ_VTOT01000064.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12636342
            Assembly: GCF_009899505.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5978)
  AUTHORS   Valat,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-AUG-2019) AVB, Anses, 31 Avenue Tony Garnier, Lyon
            69007, France
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            VTOT01000064.1.
            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          :: 25-OCT-2018
            Assembly Method        :: Unicycler v. 0.4.8-beta
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 10.0x
            Sequencing Technology  :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009899505.1-RS_2024_12_22
            Annotation Date                   :: 12/22/2024 03:01:28
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.9
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,998
            CDSs (total)                      :: 4,906
            Genes (coding)                    :: 4,705
            CDSs (with protein)               :: 4,705
            Genes (RNA)                       :: 92
            rRNAs                             :: 2, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 73 of 201
            Pseudo Genes (incomplete)         :: 149 of 201
            Pseudo Genes (internal stop)      :: 34 of 201
            Pseudo Genes (multiple problems)  :: 49 of 201
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..5978
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /submitter_seqid="36291_S17-contig_64"
                     /strain="EC36291"
                     /host="bovine"
                     /db_xref="taxon:562"
                     /geo_loc_name="France"
                     /lat_lon="48.1333 N 2.2333 W"
                     /collection_date="2014-04-08"
                     /collected_by="Anses"
     gene            complement(<1..253)
                     /locus_tag="FZC20_RS22340"
                     /old_locus_tag="FZC20_22750"
     CDS             complement(<1..253)
                     /locus_tag="FZC20_RS22340"
                     /old_locus_tag="FZC20_22750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612086.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /protein_id="WP_000165167.1"
                     /translation="MTKNTRFSPEVRQRAVRMVLESQGEYDSQWAAICSIAPKIGCTP
                     ETLRVWVRQHERDTGGGDGGLTSAERQRLKELERENRELR"
     gene            442..1026
                     /locus_tag="FZC20_RS22345"
                     /old_locus_tag="FZC20_22755"
     CDS             442..1026
                     /locus_tag="FZC20_RS22345"
                     /old_locus_tag="FZC20_22755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000517560.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000517560.1"
                     /translation="MGKMKELLFEIQEERTDEWIAENYTDAEEGTPEWDAAAQEYSWF
                     QDWMEEAAEQQYFEASLASIPDRLQDAKDELFELENLMQFNQPGIVERMAYVHCVSVL
                     DSFLMYSARALLNHPPHLQRFLQVADSLIANKEDRRKLRASKWVEQEPDTATPEKVYT
                     WRAQSLVAKKTFQSHKVIDRYFSTMLATPHEWPL"
     gene            <1248..1790
                     /locus_tag="FZC20_RS22350"
                     /old_locus_tag="FZC20_22760"
                     /pseudo
     CDS             <1248..1790
                     /locus_tag="FZC20_RS22350"
                     /old_locus_tag="FZC20_22760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001164196.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA];
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="internal stop; 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="tyrosine-type recombinase/integrase"
     gene            1972..2616
                     /locus_tag="FZC20_RS22355"
                     /old_locus_tag="FZC20_22765"
     CDS             1972..2616
                     /locus_tag="FZC20_RS22355"
                     /old_locus_tag="FZC20_22765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001144037.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_001144036.1"
                     /translation="MPVIANTHPKGGVGKTTSSVNIVGEMKSDTVDLDTHTGLSIILG
                     LRPEGKEISVKVPKTVDELIEIMTPYKNSDKTLLIDCGGFDSDLTRTAIAFADCVIVP
                     SKDSLTERIGLMHFDGVLDEISSIMGTDITAHLYLCKVNPNKKKFPKLDAILPSFKHL
                     KLMKSRISARAEFEDVIETGMGITESVHGRYSAGGKEVIALIEEINHLIENNKQ"
     gene            2703..3011
                     /locus_tag="FZC20_RS22360"
                     /old_locus_tag="FZC20_22770"
     CDS             2703..3011
                     /locus_tag="FZC20_RS22360"
                     /old_locus_tag="FZC20_22770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000030202.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="molecular chaperone GroEL"
                     /protein_id="WP_000030206.1"
                     /translation="MSKAKFSAQAEKLKNLVDSARLQTSSSAVTATVPSQPNEGTEEV
                     SGRPVAARTKAKNLKAIPLSYFEAHAELKATSKTSLDFSSYIIEAIREKLERDGAIGQ
                     "
     gene            3425..4405
                     /locus_tag="FZC20_RS22365"
                     /old_locus_tag="FZC20_22775"
     CDS             3425..4405
                     /locus_tag="FZC20_RS22365"
                     /old_locus_tag="FZC20_22775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001401593.1"
                     /GO_function="GO:0000166 - nucleotide binding [Evidence
                     IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid segregation protein ParM"
                     /protein_id="WP_000688502.1"
                     /translation="MKIFIDDGSTNIKLAWLEDGDVKTLISPNSFKPEWSFSLLDDAA
                     PANYEIDGEKFSFDPLSADAVVTTETRYQYSDVNVVAIQHALQQTGLKAQPIDVIVTL
                     PISEYLDANNQKNKQNIERKKKNVMREVRVQGSDAFVIRSVSVLPESIPAGFSVLAGL
                     EDDESLLIVDLGGTTLDVSHVRSKMTGITKTWCDPNIGVSLITSGVKEQMAVHANTRV
                     SSFQADNIIVHRNEPDYLSRRIYNAEQRESIINVINERQKLLIKRVNDVISRFTDYTH
                     VMCVGGGAEIVAEAVKNLTKVPDERFYLSSSPQFDLVMGMIKMKGGVTNE"
     gene            4398..4814
                     /locus_tag="FZC20_RS22370"
                     /old_locus_tag="FZC20_22780"
     CDS             4398..4814
                     /locus_tag="FZC20_RS22370"
                     /old_locus_tag="FZC20_22780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001278810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid partitioning/stability family protein"
                     /protein_id="WP_001278818.1"
                     /translation="MSDENKSRRCSFELFPDERTGDKIADELIANEKLKERGRFMRAM
                     LVTGAAFAAIDKRLPLLISELLTENTTLDDINKVISSVIPGAFSVEKKLLELLEKQSG
                     LHTSVDCSTPLTEQSLSRNDGEDQTRRNAENMFGDD"
     gene            complement(4816..>5783)
                     /gene="umuC"
                     /locus_tag="FZC20_RS22375"
                     /old_locus_tag="FZC20_22785"
                     /pseudo
     CDS             complement(4816..>5783)
                     /gene="umuC"
                     /locus_tag="FZC20_RS22375"
                     /old_locus_tag="FZC20_22785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001566943.1"
                     /GO_function="GO:0003684 - damaged DNA binding [Evidence
                     IEA]"
                     /GO_process="GO:0006281 - DNA repair [Evidence IEA]"
                     /note="frameshifted; 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="translesion error-prone DNA polymerase V subunit
                     UmuC"
     gene            complement(5773..>5978)
                     /locus_tag="FZC20_RS22380"
                     /old_locus_tag="FZC20_22790"
     CDS             complement(5773..>5978)
                     /locus_tag="FZC20_RS22380"
                     /old_locus_tag="FZC20_22790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000457137.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="S24 family peptidase"
                     /protein_id="WP_284696647.1"
                     /translation="GDLLVVDRAEKPQHGDIVIAEIDGEFTVKRLLLRPRPALEPVSD
                     SPEFRTLYPENICIFGVVTHVVH"
CONTIG      join(VTOT01000064.1:1..5978)
//
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