LOCUS QXHA01000960 5639 bp DNA linear BCT 13-SEP-2018 DEFINITION Escherichia coli strain S308 NODE_196_length_5575_cov_9.907444, whole genome shotgun sequence. ACCESSION QXHA01000960 QXHA01000000 VERSION QXHA01000960.1 DBLINK BioProject: PRJNA488427 BioSample: SAMN09932981 KEYWORDS WGS. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 5639) 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 5639) 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..5639 /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..543 /locus_tag="D3C88_14120" CDS <1..543 /locus_tag="D3C88_14120" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_311954.2" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="4,5-DOPA dioxygenase extradiol" /protein_id="RIB41279.1" /translation="PGSPALAQRLVELLAPVPVALDKEAWGFDHGSWGVLIKMYPDAD IPMVQLSIDSSKPAAWHFEMGRKLAALRDEGIMLVASGNVVHNLRTVKWHGDSSPYPW ATSFNEYVKANLTWQGPVEQHPLVNYLDHEGGALSNPTPEHYLPLLYVLGAWDGQEPI TIPVDGIEMGSLSMLSVQIG" gene complement(589..1260) /gene="dsbI" /locus_tag="D3C88_14125" CDS complement(589..1260) /gene="dsbI" /locus_tag="D3C88_14125" /inference="COORDINATES: similar to AA sequence:RefSeq:YP_002414186.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="protein-disulfide oxidoreductase DsbI" /protein_id="RIB41280.1" /translation="MGIKGMWKDLRTSPVDTLVRWQEQRLLWLLMAVAMGALIILAHS FFQIYLYMAPCEQCVYIRYAMFVMVIGGLVAAINPKNIILKLIGCVMAFYGSILGLKF SLKLNDIHHAVHNPDPDSLFGVQGCSTDPTFPFNLPLAQWAPNWFKPTGDCGYDAPIV PDGVTLSSTQQWFVEMYQQSEGWYLLPPWHFMNMAQACMLAFGMCLVLLVIMSGAWAL KIIRG" gene complement(1275..1943) /locus_tag="D3C88_14130" CDS complement(1275..1943) /locus_tag="D3C88_14130" /inference="COORDINATES: similar to AA sequence:RefSeq:YP_002414185.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="thiol:disulfide interchange protein DsbA/DsbL" /protein_id="RIB41281.1" /translation="MSKLGISSLFKTILLTAALAVSFTASAFTEGTDYMVLEKPIPNA DKTLIKVFSYACPFCYKYDKAVTGPVSEKVKDIVAFTPFHLETKGEYGKQASEVFAVL INKDKAAGISLFDANSQFKKAKFAYYAAYHDKKERWSDGKDPAAFIKTGLDAAGMSQA DFEAALKEPAVQETLKKWKASYDVAKIQGVPAYVVNGKYLIYTKSIKSIDAMADLIRE LASK" gene complement(1961..3757) /locus_tag="D3C88_14135" CDS complement(1961..3757) /locus_tag="D3C88_14135" /inference="COORDINATES: similar to AA sequence:RefSeq:YP_002414184.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="aryl-sulfate sulfotransferase" /protein_id="RIB41282.1" /translation="MFDKYRKTLVAGTVAITLGLSASGVMAAGFKPAPPAGQLGAVIV DPYGNAPLTALVDLDSHVISDVKVTVHGKGEKGVEISYPVGQESLKTYDGVPIFGLYQ KFANKVTVEWKENGKVMKDDYVVHTSAIVNNYMDNRSISDLQQTKVIKVAPGFEDRLY LVNTHTFTAQGSDLHWHGEKDKNAGILDAGPATGALPFDIAPFTFIVDTEGEYRWWLD QDTFYDGRDRDINKRGYLMGIRETPRGTFTAVQGQHWYEFDMMGQVLEDHKLPRGFAD ATHESIETPNGTVLLRVGKSNYRRDDGVHVTTIRDHILEVDKSGRVVDVWDLTKILDP KRDALLGALDAGAVCVNVDLAHAGQQAKLEPDTPFGDALGVGPGRNWAHVNSIAYDAK DDSIILSSRHQGVVKIGRDKQVKWILAPSKGWEKPLASKLLKPVDANGKPITCNENGL CENSDFDFTYTQHTAWISSKGTLTIFDNGDGRHLEQPALPTMKYSRFVEYKIDEKKGT VQQVWEYGKERGYDFYSPITSIIEYQADRNTMFGFGGSIHLFDVGQPTVGKLNEIDYK TKEVKVEIDVLSDKPNQTHYRALLVRPQQMFK" gene complement(4242..5402) /locus_tag="D3C88_14140" CDS complement(4242..5402) /locus_tag="D3C88_14140" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_005123077.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="glutathionylspermidine synthase family protein" /protein_id="RIB41283.1" /translation="MERVSITERPDWREKAHEYGFNFHTMYGEPYWCEDAYYKLTLAQ VEKLEEVTAELHQMCLKVVEKVIASDELMTKFRIPKHTWSFVRQSWLTHQPSLYSRLD LAWDGTGEPKLLENNADTPTSLYEAAFFQWIWLEDQLNAGNLPEGSDQFNSLQEKLID RFVELREQYGFQLLHLTCCRDTVEDRGTIQYLQDCATEAEIATEFLYIDDIGLGEKGQ FTDLQDQVISNLFKLYPWEFMLREMFSTKLEDAGVRWLEPAWKSIISNKALLPLLWEM FPNHPNLLPAYFAEDDHPQMEKYVVKPIFSREGANVSIIENGKTIAAAEGPYGEEGMI VQQFHPLPKFGDSYMLIGSWLVNDQPAGIGIREDRALITQDMSRFYPHIFVE" gene complement(5408..>5639) /locus_tag="D3C88_14145" CDS complement(5408..>5639) /locus_tag="D3C88_14145" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_417509.3" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=2 /transl_table=11 /product="DUF1190 domain-containing protein" /protein_id="RIB41284.1" /translation="SSKNPASPAYGKYTDATGKNYGAAQPGRTMTVPKTAMAPKPATT TTVTRGGFGESVAKQSTMQRSATGTSSRSMGG" BASE COUNT 1396 a 1328 c 1383 g 1532 t ORIGIN 1 ccgggttcgc ctgcgctggc acagcgtctg gttgagctgt tagcgccggt tcctgtggcg 61 ctggataaag aagcctgggg ctttgaccac ggttcctggg gagtgctgat taagatgtac 121 cctgacgccg atatcccgat ggtgcagttg agtatcgaca gtagcaaacc tgccgcctgg 181 catttcgaaa tggggcgcaa actcgcggcg ctgcgtgatg aagggataat gttggtcgcc 241 agtggcaacg tggtgcataa cctgcgtaca gtgaagtggc acggtgatag ttcaccgtat 301 ccgtgggcga cgtcgtttaa tgagtatgtg aaagcgaatc tgacgtggca agggccagtg 361 gaacaacatc ctctggtgaa ttatctcgac catgaaggtg gcgcgttatc gaacccaacg 421 ccagagcact atctgccgtt gttgtatgtc ttaggggcgt gggatgggca ggagccaatt 481 accattccgg tcgatggtat agaaatgggc agtttaagta tgctgtcggt gcagataggt 541 taataaaaga acccgaagcc agaacgactg gcttcgggtg ttgctgagtt agcctctgat 601 gattttaagc gcccatgcgc cactcataat gaccagcagc accagacaca taccaaaagc 661 cagcatacaa gcctgagcca tattcataaa atgccatggt ggtagcagat accagccttc 721 agattgctga tacatttcca caaaccactg ttgcgtgctg ctcagtgtga cgccatcagg 781 aacgattggt gcgtcatagc cacaatcccc ggtaggcttg aaccaatttg gtgcccactg 841 tgccagcggc aggttaaagg gaaaagtggg atcggtagag caaccctgta cgccaaacag 901 tgaatcggga tccggattat gtactgcatg gtggatatcg ttcagtttga gcgaaaactt 961 cagtcccaaa atgctgccgt aaaatgccat cacgcagcca attagcttta ggatgatgtt 1021 ctttgggttg atcgctgcaa ccaatcctcc aataaccatc acaaacatgg cgtagcgaat 1081 gtatacacat tgctcacagg gtgccatgta gagatagatc tggaagaaag agtgcgccag 1141 gataattaac gcgcccatcg caacggccat taacaaccac aacaagcgtt gctcctgcca 1201 tctgaccagt gtgtcaactg gtgatgtgcg aagatctttc cacattccct taatacccat 1261 agcctgtttc cctgttattt gcttgctaac tcacggataa ggtctgccat cgcgtcgatg 1321 gatttgatgc tcttggtgta gatcaagtac ttaccattaa cgacataggc tggaactccc 1381 tggattttgg cgacatcata agaggctttc cattttttca gtgtttcttg aaccgctggt 1441 tctttcagtg ccgcttcaaa atccgcctga ctcatacctg cggcatccag accggttttg 1501 ataaaagcag ccggatcttt accgtcagac cagcgttctt ttttgtcgtg ataagccgcg 1561 tagtaggcaa acttggcttt cttaaactga gagttagcat caaataagga aatgcctgct 1621 gctttatctt tattgatcaa gaccgcaaag acttcgcttg cttgtttgcc gtattcacct 1681 tttgtttcca gatggaatgg cgtgaaagca acgatatctt tcactttttc cgataccgga 1741 ccggtaaccg ctttgtcgta cttgtaacag aacgggcagg cgtagctaaa taccttaatc 1801 agcgttttgt cggcattcgg aattggtttt tccagaacca tgtaatccgt gccttcggta 1861 aatgcagaag cggtaaatga aaccgccaga gctgcggtaa gcagtatggt tttaaatagt 1921 gatgagatcc ctaatttcga catttttatt cccttcttaa ttatttgaac atctgttgtg 1981 gacggactaa cagcgcacgg tagtgagtct gattgggttt atctgacagc acgtcgattt 2041 ccactttcac ttctttggtt ttgtaatcga tttcgttcaa cttaccgacg gttggctgcc 2101 cgacatcgaa caaatgaata gaaccaccga agccaaacat ggtgttacgg tcggcttgat 2161 attcaatgat ggaggtaatc gggctataga aatcgtagcc acgttcttta ccgtattccc 2221 acacttgctg aacggtgcct ttcttctcat caatcttata ttccacaaag cgagagtatt 2281 tcatggttgg taaggcaggt tgttccagat gacgcccatc gccattatca aaaatggtga 2341 gcgttccttt gctggaaatc caggcggtat gctgggtgta ggtaaagtcg aagtctgagt 2401 tttcgcacag gccattttcg ttacaggtaa ttggcttacc gttagcatca accggtttca 2461 gcagcttgct ggccagcggt ttttcccaac ctttagaggg cgcaaggatc catttcactt 2521 gcttatcacg accaatcttc acaacaccct ggtggcgaga ggagaggatg atagagtcat 2581 cttttgcgtc ataggcgata gagttcacgt gcgcccagtt gcggcctggc cctacaccca 2641 gcgcgtcgcc gaacggtgta tctggttcca gttttgcctg ttgtcctgca tgggcaaggt 2701 caacgttaac gcaaactgca cctgcatcca gcgcgccgag cagtgcatcg cgtttcggat 2761 cgaggatctt ggtcagatcc catacatcga caacgcgacc agatttatcg acttcgagga 2821 tatggtcacg aatggtggtg acgtgtacgc cgtcatcgcg acgatagtta ctcttaccta 2881 cgcgcaacag taccgtgcca tttggcgtct caatggactc atgagtggcg tcagcaaatc 2941 cgcgcggtag tttgtgatct tcgagcacct gccccatcat gtcgaactcg taccagtgct 3001 gaccttgtac agcggtaaag gtgccgcgtg gcgtttcgcg gatacccatc agataaccac 3061 gcttgttgat atcgcggtca cgaccatcgt agaaagtgtc ttgatccagc caccagcggt 3121 attcaccttc ggtatcgacg atgaaagtaa agggcgcgat atcaaaaggg agtgcgccgg 3181 ttgccggacc cgcatcaagg ataccggcat ttttatcttt ctcaccatgc cagtggagat 3241 cggaaccttg ggcggtaaag gtgtgggtat taaccagata gaggcgatct tcaaaacccg 3301 gtgcgacttt aataactttg gtctgttgta aatcggagat agagcggtta tccatgtaat 3361 tattgacgat ggccgaagtg tgcaccacat aatcatcttt catgaccttg ccgttttctt 3421 tccactcaac ggtcactttg ttagcaaatt tctgataaag accaaaaatc ggtacaccat 3481 cgtaagtttt tagtgattcc tgacccacgg gatagctgat ttctacgcct ttttcgccct 3541 tcccatggac ggtaactttg acgtcagaaa taacatggct atctaagtca accaaagcgg 3601 tcagtggtgc attgccgtag ggatcgacaa tgaccgcacc cagttgcccg gcaggtggcg 3661 ctggtttaaa acccgcagcc atcacccccg atgctgacaa acccagggtt atcgccacag 3721 ttccggctac gagtgttttt ctatatttat caaacatgga tatatctcct tatataacgc 3781 aaatatataa taatgatgaa tatcgactgt tgagagggtg ctaataaatt cgttacgtga 3841 atataaatat taattcaata aagagtgaga atgcttttgt gtttctttta aatatgttgt 3901 tattcggtga aacaaatatt tatgtttaat ggatagtagg ggggcaatat atcaatcaca 3961 atgttcaata ctgtgtagtg tgatccctgc aacattgttt tttaattatt aaatttaaat 4021 ctggtgagat aaaagtaaag tatttaaata atatcaaata gttatgttgt gatgtattca 4081 cttactttaa ttacaatatc gcttgcatat gacgatttaa cattaaattg agtattaatg 4141 ttaaataaag gttggatatg tatgtgttta tatattgatg ggagttatga atggtggatt 4201 ataagagatt gccccgctta tcggggcaat attaagctgt attactcaac aaaaatatgc 4261 ggataaaacc gagacatatc ctgggtgatc aatgcacggt cttcacgaat gccaattccg 4321 gcaggttgat cgttcaccag ccagctacca atcagcatat agctgtcgcc gaatttcggt 4381 aacgggtgga attgctgaac aatcatccct tcttcgccat acggaccttc cgctgctgca 4441 atggttttgc cgttctcaat gatcgacacg tttgcgcctt cacgggagaa gatcggttta 4501 accacatatt tttccatttg cggatgatca tcttccgcaa aataagcggg cagcaggttc 4561 gggtgattcg ggaacatctc ccacagtagc ggtagaagcg ctttgttgga gataatgctc 4621 ttccacgccg gttccagcca gcgtacgcct gcatcctcca gcttggtgga gaacatctca 4681 cgcaacataa attcccacgg atacagcttg aacaggttgg aaatcacctg atcctgtaaa 4741 tccgtgaact gacctttttc acctaacccg atatcgtcga tgtagaggaa ctcggtagcg 4801 atttcagctt ccgtcgcgca gtcctgcaaa tactgaatgg ttccgcgatc ttccaccgtg 4861 tcgcgacagc aggtgagatg cagcaactgg aagccatact gttcacgcag ctcaacgaag 4921 cgatcgatca gcttttcttg caaactgtta aactggtcgc tgccctccgg caagttaccg 4981 gcgttaagct gatcttccag ccagatccac tgaaagaacg ccgcctcgta tagtgacgtt 5041 ggcgtatcgg cgttattttc cagaagttta ggttcgccag tgccatccca cgccagatca 5101 agacgcgaat aaagcgatgg ctggtgcgtc agccatgact ggcgcacaaa actccaggtg 5161 tgttttggaa tgcggaattt ggtcatcagc tcatcgctgg cgatcacttt ttccaccact 5221 ttcaggcaca tctggtgcag ttcggcggtg acttcttcca gcttttcaac ctgggcgagg 5281 gtcaacttgt agtaagcatc ttcacaccag tacggctcgc cgtacatggt gtgaaaattg 5341 aaaccgtatt cgtgggcttt ttcgcgccag tccgggcgct cggtaatact gactctttcc 5401 atcggtatca gccacccatt gaacgagaag aggtgccggt tgcgctacgc tgcatagtgc 5461 tttgtttggc aacagattca ccaaaaccgc cacgggtaac agtagtagtg gtcgccggtt 5521 ttggtgccat tgccgtcttc ggtacggtca tggtgcggcc tggctgggct gcgccatagt 5581 ttttaccggt cgcgtcggta tatttaccgt aagccgggct ggccgggttt ttcgaggag //