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Escherichia coli strain A12-3-R 69, whole genome shotgun sequence

NCBI Reference Sequence: NZ_JBJHSP010000069.1

FASTA Graphics 

LOCUS       NZ_JBJHSP010000069      9615 bp    DNA     linear   CON 26-NOV-2024
DEFINITION  Escherichia coli strain A12-3-R 69, whole genome shotgun sequence.
ACCESSION   NZ_JBJHSP010000069 NZ_JBJHSP010000000
VERSION     NZ_JBJHSP010000069.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN44775132
            Assembly: GCF_045258375.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 9615)
  AUTHORS   Zhang,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-NOV-2024) School of Public Health, Hangzhou Medical
            College, Tianmu Mountain Road, Hangzhou, Zhejiang 310000, China
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            JBJHSP010000069.1.
            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. July-2024
            Genome Representation  :: Full
            Expected Final Version :: No
            Genome Coverage        :: 205.0x
            Sequencing Technology  :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_045258375.1-RS_2024_11_25
            Annotation Date                   :: 11/25/2024 13:53:31
            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)                     :: 5,229
            CDSs (total)                      :: 5,134
            Genes (coding)                    :: 4,800
            CDSs (with protein)               :: 4,800
            Genes (RNA)                       :: 95
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 334
            CDSs (without protein)            :: 334
            Pseudo Genes (ambiguous residues) :: 0 of 334
            Pseudo Genes (frameshifted)       :: 97 of 334
            Pseudo Genes (incomplete)         :: 252 of 334
            Pseudo Genes (internal stop)      :: 43 of 334
            Pseudo Genes (multiple problems)  :: 54 of 334
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..9615
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="A12-3-R"
                     /host="animal"
                     /db_xref="taxon:562"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2024-10"
     repeat_region   19..779
                     /inference="COORDINATES: alignment:CRISPRCasFinder:4.3.2"
                     /rpt_family="CRISPR"
                     /rpt_type=direct
                     /rpt_unit_range=19..47
                     /rpt_unit_seq="cggtttatccccgctggcgcggggaacac"
     gene            complement(876..1169)
                     /gene="cas2e"
                     /locus_tag="ACJEG2_RS24370"
                     /old_locus_tag="ACJEG2_24370"
     CDS             complement(876..1169)
                     /gene="cas2e"
                     /locus_tag="ACJEG2_RS24370"
                     /old_locus_tag="ACJEG2_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311635.1"
                     /GO_function="GO:0004521 - RNA endonuclease activity
                     [Evidence IEA]"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I-E CRISPR-associated endoribonuclease
                     Cas2e"
                     /protein_id="WP_000061856.1"
                     /translation="MSMIVVVTENVPPRLRGRLAIWLLEVRAGVYVGDTSKRIREMIW
                     QQISQLAGCGNVVMAWATNTESGFEFQTWGENRRIPVDLDGLRLVSFLPVDNQ"
     gene            complement(1166..>1462)
                     /locus_tag="ACJEG2_RS24375"
                     /old_locus_tag="ACJEG2_24375"
                     /pseudo
     CDS             complement(1166..>1462)
                     /locus_tag="ACJEG2_RS24375"
                     /old_locus_tag="ACJEG2_24375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311636.1"
                     /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="subtype I-E CRISPR-associated endonuclease Cas1"
     gene            <1459..2124
                     /gene="casA"
                     /locus_tag="ACJEG2_RS24380"
                     /old_locus_tag="ACJEG2_24380"
                     /gene_synonym="cse1"
                     /pseudo
     CDS             <1459..2124
                     /gene="casA"
                     /locus_tag="ACJEG2_RS24380"
                     /old_locus_tag="ACJEG2_24380"
                     /gene_synonym="cse1"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311641.1"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /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="type I-E CRISPR-associated protein Cse1/CasA"
     gene            2121..2657
                     /gene="casB"
                     /locus_tag="ACJEG2_RS24385"
                     /old_locus_tag="ACJEG2_24385"
                     /gene_synonym="cse2"
     CDS             2121..2657
                     /gene="casB"
                     /locus_tag="ACJEG2_RS24385"
                     /old_locus_tag="ACJEG2_24385"
                     /gene_synonym="cse2"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311640.1"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I-E CRISPR-associated protein Cse2/CasB"
                     /protein_id="WP_000029329.1"
                     /translation="MSIVKEEHKATLRKWHEELQEKRGERASLRRSTTVNDVCLTDGF
                     RLFLKNRQIKWQDEPEWRITALALIAAVSANVKAIDERQPFAAQLAAVMSKGRFTRLS
                     AVKTPDELLRQLRRAVRLLNGSVNLDSLAEGVFRWCQESDDLLNHHRRQQRPTEFIRI
                     RWALEYYQAGDADNEQNQ"
     gene            2669..3724
                     /gene="cas7e"
                     /locus_tag="ACJEG2_RS24390"
                     /old_locus_tag="ACJEG2_24390"
     CDS             2669..3724
                     /gene="cas7e"
                     /locus_tag="ACJEG2_RS24390"
                     /old_locus_tag="ACJEG2_24390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311639.1"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I-E CRISPR-associated protein
                     Cas7/Cse4/CasC"
                     /protein_id="WP_000206450.1"
                     /translation="MTTFIQLHLLTAYPAANLNRDDTGAPKTVVLGGATRLRVSSQSL
                     KRAWRTSALFEQALAGHIGIRSGRIAREAATILIEKGIEEKKAIEWAAKIADYLGKAK
                     NDKKPKDPLTNAETEQLVHISPAEFDAVKVLAHQLAEEKRAPKEEDLALLRKDRMAVD
                     IAMFGRMLANKPEFNVEAACQVAHAFGVSETIVEDDFFTAVDDLRQASEDAGAGHLGE
                     TGFGSALFYTYICIDKDLLVENLGGDEALANQTIRAFTEAALKVSPTGKQNSFASRAY
                     ASWALAEKGTDQPRSLAAAFYEPINGTRQLEVAVQRITTLRENMNTVYEQKTDYASFD
                     VMNKQGSMKDVLDFICA"
     gene            3735..4481
                     /gene="cas5e"
                     /locus_tag="ACJEG2_RS24395"
                     /old_locus_tag="ACJEG2_24395"
     CDS             3735..4481
                     /gene="cas5e"
                     /locus_tag="ACJEG2_RS24395"
                     /old_locus_tag="ACJEG2_24395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311638.1"
                     /GO_function="GO:0003723 - RNA binding [Evidence IEA]"
                     /GO_process="GO:0051607 - defense response to virus
                     [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I-E CRISPR-associated protein Cas5/CasD"
                     /protein_id="WP_348911811.1"
                     /translation="MSQYLIFQLHGPMASWGVDAPGEVRHTHELPSRSALLGLLAARV
                     GIRRDDTERLNAFNRHYSLVVCASRNPRWARDYHTVQMPKEVRKARYFSRREELSDPE
                     LLSAIISRRDYYTDAWWMVAVATTPDAPYSLEQLQDGLRHPVFQLYLGRKSHPLALPL
                     APLLLEGNASDVLRNAYQQYQDRFRELKVSLPKLQDECWWEGEHDGLVASKILRRRDV
                     PLNRQQWLFGERTINQGPWLSKEEPCTSQE"
     gene            4463..5113
                     /gene="cas6e"
                     /locus_tag="ACJEG2_RS24400"
                     /old_locus_tag="ACJEG2_24400"
     CDS             4463..5113
                     /gene="cas6e"
                     /locus_tag="ACJEG2_RS24400"
                     /old_locus_tag="ACJEG2_24400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000281458.1"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I-E CRISPR-associated protein
                     Cas6/Cse3/CasE"
                     /protein_id="WP_261629466.1"
                     /translation="MYLSRITLHTGQLSPAQLLHLVDRGEYVMHQWLWDLFPGGKERQ
                     FLYRREELQGAFRFFVLSQERPAESETFTIECRSFTPELSTGQQLCFNLRANPTICKA
                     GKRHDLLMEAKRQVRGQAEGSDVWLHQQQAALDWLAAQGERSGFTLLDTSVDAYRQQQ
                     LRRENSWQLIQFSSVDYTGMLTVTDPRLFLQRLSQGYGKSRAFGCGLMLIKPGAEA"
     gene            5110..>5748
                     /gene="cas1e"
                     /locus_tag="ACJEG2_RS24405"
                     /old_locus_tag="ACJEG2_24405"
                     /pseudo
     CDS             5110..>5748
                     /gene="cas1e"
                     /locus_tag="ACJEG2_RS24405"
                     /old_locus_tag="ACJEG2_24405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311636.1"
                     /GO_function="GO:0004520 - DNA endonuclease activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]"
                     /GO_process="GO:0051607 - defense response to virus
                     [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat
                     elements [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="type I-E CRISPR-associated endonuclease Cas1e"
     gene            complement(<5735..6637)
                     /gene="casA"
                     /locus_tag="ACJEG2_RS24410"
                     /old_locus_tag="ACJEG2_24410"
                     /gene_synonym="cse1"
                     /pseudo
     CDS             complement(<5735..6637)
                     /gene="casA"
                     /locus_tag="ACJEG2_RS24410"
                     /old_locus_tag="ACJEG2_24410"
                     /gene_synonym="cse1"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311641.1"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [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="type I-E CRISPR-associated protein Cse1/CasA"
     gene            complement(6735..9434)
                     /locus_tag="ACJEG2_RS24415"
                     /old_locus_tag="ACJEG2_24415"
     CDS             complement(6735..9434)
                     /locus_tag="ACJEG2_RS24415"
                     /old_locus_tag="ACJEG2_24415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233973.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CRISPR-associated helicase/endonuclease Cas3"
                     /protein_id="WP_001233949.1"
                     /translation="MRKYPLSLLKDKNIVTFFDFWGKTRRGEKDGGDDYHLLCWHSLD
                     VAAMGYLMVKRNCFGLADYFRQLGISDKEQAAQFFAWLLCWHDIGKFARSFQQLYLPP
                     ELKIQEGARKNYEKISHSTLGYWLWNHYLSECQELLPSSSLSPRKLRRVIEMWMPVTT
                     GHHGRPPDRMDELDNFLPEDKAAARDFLLEIKPLFPLIEIPAFWDDDEGIELIKHLSW
                     YISATVVLADWTGSSTRFFPRVAHPMDIKGYWQKTLIQAQNALTVFPLKAKVAPFNGI
                     NTLFPFIENPTPLQQKVLDLDISQQGPQLFILEDVTGAGKTEAALILAHRLIAAGKAQ
                     GLFFGLPTMATANAMYDRLVKTWLAFYSPESRPSLVLAHSARTLMDRFNESLWSGDLV
                     GSEEPDEQTFSQGCAAWFADSNKKALLAEIGVGTLDQAMMAVMPFKHNNLRLLGLSNK
                     ILLADEIHACDAYMSCILEGLIERQARGGNSVILLSATLSQQQRDKLVAAFARGTEGQ
                     QEAPFLEKDDYPWLTHVTKSDVNSHRVATRKDVERSVSVGWLHSEQECIARIESAVSQ
                     GKCIAWIRNSVDDAIKVHRQLLARGVIPASSLSLFHSRFAFSDRQRIETETLARFGKY
                     CSLQRASQVIVCTQVIEQSVDIDLDEMISDLAPVDLLIQRAGRLQRHIRDINGQLKRD
                     GKDERSPPELLILAPVWDDSPGDEWFGSAMRNSAFVYPDHGRIWLTQRVLREQGAIQM
                     PHAARLLIESVYGEDVVMPEGFARSEQEQVGKYYCDRAMAKKFVLNFRPGYAANINDY
                     LPEKLSTRLAEESVSLWLATCIDGVVKPYATGAHAWEMSVVRVRRSWWKKHRDEFSLL
                     EGEAFRLWCIEQRQDPEMANVILVNDDESCGYSATEGLIGKVG"
CONTIG      join(JBJHSP010000069.1:1..9615)
//
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