LOCUS QXHA01000285 3461 bp DNA linear BCT 13-SEP-2018 DEFINITION Escherichia coli strain S308 NODE_1288_length_3397_cov_12.695909, whole genome shotgun sequence. ACCESSION QXHA01000285 QXHA01000000 VERSION QXHA01000285.1 DBLINK BioProject: PRJNA488427 BioSample: SAMN09932981 KEYWORDS WGS. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 3461) AUTHORS Geslain,G., Birgy,A., Adiba,S., Magnan,M., Courroux,C., Levy,C., Cohen,R., Bidet,P. and Bonacorsi,S. TITLE Genome sequencing of strains of the most prevalent clonal group of O1:K1:H7 Escherichia coli that causes neonatal meningitis in France JOURNAL BMC Microbiol. (2018) In press REFERENCE 2 (bases 1 to 3461) AUTHORS Geslain,G., Birgy,A., Adiba,S., Magnan,M., Courroux,C., Levy,C., Cohen,R., Bidet,P. and Bonacorsi,S. TITLE Direct Submission JOURNAL Submitted (31-AUG-2018) Microbiologie, Hopital Robert-Debre, APHP, 48 bd Serurier, Paris 75019, France COMMENT Bacteria available from Pathogen.cl. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Assembly-Data-START## Assembly Method :: SPAdes v. 8.0.2 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 16,40x Sequencing Technology :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 09/04/2018 14:34:05 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set; GeneMarkS+ Annotation Software revision :: 4.6 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total) :: 6,865 CDS (total) :: 6,787 Genes (coding) :: 6,492 CDS (coding) :: 6,492 Genes (RNA) :: 78 rRNAs :: 1, 3, 1 (5S, 16S, 23S) complete rRNAs :: 1, 1 (5S, 23S) partial rRNAs :: 3 (16S) tRNAs :: 67 ncRNAs :: 6 Pseudo Genes (total) :: 295 Pseudo Genes (ambiguous residues) :: 3 of 295 Pseudo Genes (frameshifted) :: 122 of 295 Pseudo Genes (incomplete) :: 124 of 295 Pseudo Genes (internal stop) :: 78 of 295 Pseudo Genes (multiple problems) :: 30 of 295 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..3461 /organism="Escherichia coli" /mol_type="genomic DNA" /strain="S308" /serotype="O1:K1" /isolation_source="cerebrospinal fluid" /host="Homo sapiens" /db_xref="taxon:562" /geo_loc_name="France: Limoges" /lat_lon="48 N 2 W" /collection_date="2009" /collected_by="Microbiology dpt, Hospital Robert-Debre, 48 bd serurier, 75019 Paris" gene <1..409 /locus_tag="D3C88_04880" CDS <1..409 /locus_tag="D3C88_04880" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_310812.1" /note="catalyzes th removal of D-alanine and attachment of the murein lipoprotein to the peptidoglycan tetrapeptide chain; Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=2 /transl_table=11 /product="L,D-transpeptidase" /protein_id="RIB43022.1" /translation="PMGLYAIYIGKLYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLF DNVPVGTRVQIIDQPVKYTTEPDGSKWLEVHEPLSRNRAEYESDRKVPLPVTPSLRAF INGQEVDVNRANAALQHRSGMPVQISSGSRQMF" gene 728..1126 /locus_tag="D3C88_04885" CDS 728..1126 /locus_tag="D3C88_04885" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000906673.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="RIB43023.1" /translation="MLINEELVDKIDTKNYGDGSNNVFVIWTLSLKSSTKSECFKFLG FVHLQSVLVEISSSPEKYYKLRIHQERVMEGMMPEEPKAIVIEDTEWGCIHSQYHYQD KDPAIITCIVNVNNTDLIATELVNSVLNTS" gene complement(1216..1416) /locus_tag="D3C88_04890" /pseudo CDS complement(1216..1416) /locus_tag="D3C88_04890" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_012477168.1" /note="incomplete; partial in the middle of a contig; missing start; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="IS3 family transposase" gene complement(1434..2284) /locus_tag="D3C88_04895" /pseudo CDS complement(1434..2284) /locus_tag="D3C88_04895" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_012543393.1" /note="frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="IS3 family transposase" gene complement(2430..3164) /locus_tag="D3C88_04900" CDS complement(2430..3164) /locus_tag="D3C88_04900" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001217110.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="colibactin biosynthesis phosphopantetheinyl transferase ClbA" /protein_id="RIB43024.1" /translation="MRIDILIGHTSFFHQTSRDNFLHYLNEEEIKRYDQFHFVSDKEL YILSRILLKTALKRYQPDVSLQSWQFSTCKYGKPFIVFPQLAKKIFFNLSHTIDTVAV AISSHCELGVDIEQIRDLDNSYLNISQHFFTPQEATNIVSLPRYEGQLLFWKMWTLKE AYIKYRGKGLSLGLDCIEFHLTNKKLTSKYRGSPVYFSQWKICNSFLALASPLITPKI TIELFPMQSQLYHHDYQLIHSSNGQN" gene complement(3165..3377) /locus_tag="D3C88_04905" CDS complement(3165..3377) /locus_tag="D3C88_04905" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000357141.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="colibactin biosynthesis LuxR family transcriptional regulator ClbR" /protein_id="RIB43025.1" /translation="MDKFKEKNPLSLRERQVLRMLAQGDEYSQISHNLNISINTVKFH VKNIKHKIQARNTNHAIHIANRNEII" BASE COUNT 961 a 706 c 749 g 1045 t ORIGIN 1 ccccatgggg ctgtacgcga tttatattgg caagttgtat gccatccacg gtaccaatgc 61 caattttggt attgggctcc gtgtaagtca gggctgtatt cgtctgcgta atgacgatat 121 caaatatctg tttgataatg ttcctgtagg cactcgtgta caaattattg atcagccagt 181 gaaatacaca acggaaccgg atggttcaaa gtggctggaa gttcatgagc cgctgtcgcg 241 caatcgtgca gaatatgagt ctgaccgaaa agtgccattg ccggtaaccc catctttgcg 301 ggcgtttatc aacgggcaag aagttgatgt aaatcgcgca aatgctgcgt tgcaacatcg 361 atcgggaatg cctgtgcaaa ttagttctgg ttcaagacag atgttttaag agcgttggta 421 attagaaagt aaaaagcctg ctcgaaagca ggcttttttg aatttggctc ctctgactgg 481 gatcgccttt gccagtaagt ggctaataag taagctaaac cagagttatc ttcctgtcaa 541 gaccaccaga atgaccacca ataggagctg gctacataaa tttggtttga gcttccctac 601 tgcatgtggt gatagttact atagtgtccc tacgtgggaa gcgctgatcc tctcccctag 661 tggaactgtg tctaaagagc gataacagtc cgctcagggc gtgaagcgga agttgctaaa 721 tcagtctatg ttaatcaacg aggagctggt agataagatt gacactaaaa attatggtga 781 tggttccaat aacgtgtttg ttatctggac tttatcatta aaatcctcta caaaatccga 841 gtgttttaaa tttctaggct tcgtacatct acaatctgta ctcgttgaaa tttcttcatc 901 tccagagaag tactacaagt tacgtatcca tcaagaacgt gttatggaag gtatgatgcc 961 tgaagaacca aaagccatag ttatagaaga tactgagtgg gggtgtatcc actcgcagta 1021 tcactaccaa gataaagatc ctgcgataat aacatgtatc gtaaacgtaa ataatactga 1081 cttaatagct acagagcttg tgaactcagt gttgaataca tcctgaattt cttctctcga 1141 tgctggtaca cagcgatcat ataaagttac cgcgaaagaa acgactgatc ctaccctcgt 1201 aatatggaca ctgctctaag cgaggttctg gttttcaaat tgttccggag tgagaccgcc 1261 acaccaactg tgccgtcgcc agcgactgta atcacattcg atataattaa acaccgttgc 1321 ccgcattatt tcccggctga taaagtgttc tccatggaga cattccactt tcagtgaatg 1381 aaagaagctt tccacgcagg cattatcgta gcagcagtgt aaatagaccc attttagttc 1441 catacacttt ttgagatccc ggccaaataa tggcgctgtc ggtattcctc cggtgtcata 1501 ttattcagcg attcatgcgg gcgttcacag ttatattttg ataaccattt ttcagtgatt 1561 tcccgtactt cattcagcgt tctgaacaga taaaaatcga gtatttctgt tcggtatgtc 1621 cggttaaagc gctcaatgaa agcgttctgc gtcggcttac ccggctggat aaactccagt 1681 tttattgcat gtttctctgc ccattcagcc agtgccaggg agataaattc cgggccgtta 1741 tccagacgaa gcatggccgg atagccacgg tttgccgcga tcctgtcgag tacacggacc 1801 actcgctgag ctggcagatt cagatcgatt tcaatcgaca atgcctcacg gttaaaatca 1861 tcaacgacat tgaacatgcg aaaacgacgg ccacagacca gggcatcatg cataaaatcg 1921 acagaccagc tcaggttcag actccggcag gcctgacgga tactgagttc gaacgtcgtt 1981 atcagatgag taaccagctc acgcttaaag gctggtttta aagctttttt tcgataacgt 2041 ctttcagcgc ccggttctcc agactcaggt cggcaaacat ttgttttaga cggcggttct 2101 cgtcctcaag atccttgatt ttcttaatat cagaagcctc catgccgccg tatttggact 2161 tccagttgta ataggtggct tcagagattc cggcctcgcg acagacatct ttaacagttc 2221 gtccggcttc aaccgactta atcacggcga tgatctgatg ctcagtaaaa cgggctttac 2281 gcatagcgct ctccttcgtt ggcagattga ttatgccgga tgatctctaa atgtgaatgg 2341 cacgattatg cgggatactt acaccaccga cggaatatga aaatcaatat tatcgacggc 2401 tcagaagtgt ctagattatc cgtggcgatt caattctgcc catttgacga atgaattagc 2461 tgatagtcgt ggtgataaag ttgggactgc ataggaaata gctcaatagt tattttaggg 2521 gtgatgagtg gagaggctaa tgcgagaaat gagttacata ttttccattg agagaaataa 2581 acaggtgaac ctctatattt tgaagttagt tttttatttg ttaaatgaaa ttcaatacaa 2641 tccagtccta aagataggcc tttacctcga tatttgatgt aagcttcttt gagcgtccac 2701 attttccaaa aaagtaattg accttcataa cgaggaagtg aaactatgtt agtagcttcc 2761 tgtggagtaa aaaaatgctg actgatattc agataagagt tgtctaaatc tcttatttgt 2821 tcaatatcga caccaagctc gcagtgagaa ctaatagcaa cggctactgt atctatagta 2881 tgggaaaggt taaaaaaaat cttttttgcc aactgaggaa aaactataaa tggtttgcca 2941 tatttgcacg tactaaattg ccatgattgt aatgagacat caggttgata tctttttagt 3001 gctgttttga gcaggatacg gcttaaaata tagagttctt tatcactcac aaaatgaaac 3061 tgatcatagc gttttatttc ttcctcattg agatagtgaa ggaagttatc tctactggtt 3121 tgatgaaaaa aactagtatg tccaattaat atatcaatcc tcatttagat aatctcattc 3181 ctgttagcaa tgtgtatagc gtgattcgta ttccgagctt gtattttatg tttgatgttt 3241 ttcacatgaa actttactgt gtttattgat atgttaagat tatgtgatat ttgagagtac 3301 tcatcacctt gtgccagcat gcgcaatact tgtctttcac gcagagataa cgggtttttt 3361 tctttgaact tatccatgtt tccccccatc ctgaatggta tctgtgtatc tgtgtatctg 3421 tgtatctgtg tatctgtgta tctgtgtatc tgtgtatctg t //