LOCUS AAKSUE010000071 4294 bp DNA linear BCT 18-SEP-2019 DEFINITION Salmonella enterica subsp. enterica serovar Montevideo strain FSIS11813078 SAMN09866451-rid6478093.denovo.73, whole genome shotgun sequence. ACCESSION AAKSUE010000071 AAKSUE010000000 VERSION AAKSUE010000071.1 DBLINK BioProject: PRJNA242847 BioSample: SAMN09866451 Sequence Read Archive: SRR7724245 KEYWORDS WGS; GMI. SOURCE Salmonella enterica subsp. enterica serovar Montevideo ORGANISM Salmonella enterica subsp. enterica serovar Montevideo Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella. REFERENCE 1 (bases 1 to 4294) CONSRTM GenomeTrakr network: Whole genome sequencing for foodborne pathogen traceback TITLE Direct Submission JOURNAL Submitted (21-AUG-2018) Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5100 Paint Branch Pkwy, College Park, MD, USA COMMENT This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'. 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 Date :: 21-AUG-2018 Assembly Method :: SKESA v. 2.2 Assembly Name :: PDT000365624.1 Long Assembly Name :: NCBI Pathogen Detection Assembly PDT000365624.1 Genome Coverage :: 118x Sequencing Technology :: ILLUMINA ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Date :: 08/22/2018 04:45:33 Annotation Method :: Best-placed reference protein set; GeneMarkS+ Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Provider :: NCBI Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Annotation Software revision :: 2.1 Genes (total) :: 4,800 CDS (total) :: 4,705 Genes (coding) :: 4,537 CDS (coding) :: 4,537 Genes (RNA) :: 95 rRNAs :: 5, 3, 1 (5S, 16S, 23S) complete rRNAs :: 5 (5S) partial rRNAs :: 3, 1 (16S, 23S) tRNAs :: 73 ncRNAs :: 13 Pseudo Genes (total) :: 168 Pseudo Genes (ambiguous residues) :: 0 of 168 Pseudo Genes (frameshifted) :: 86 of 168 Pseudo Genes (incomplete) :: 72 of 168 Pseudo Genes (internal stop) :: 55 of 168 Pseudo Genes (multiple problems) :: 41 of 168 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..4294 /organism="Salmonella enterica subsp. enterica serovar Montevideo" /mol_type="genomic DNA" /submitter_seqid="SAMN09866451-rid6478093.denovo.73" /strain="FSIS11813078" /serovar="Montevideo" /isolation_source="comminuted beef" /sub_species="enterica" /db_xref="taxon:115981" /geo_loc_name="USA: TX" /collection_date="2018" /collected_by="USDA-FSIS" /note="subgroup: enterica" gene complement(40..762) /locus_tag="D0215_23495" CDS complement(40..762) /locus_tag="D0215_23495" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_455139.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="fimbriae biosynthesis regulator FimY" /protein_id="ECV0722576.1" /translation="MRSVPRRERHRRLRNAKDCACRYHSPTPQIFDRLELLDQQLNYA LPVGIISQAIITTDNYLGYSLSHYLFSGKRTAAFRSLDDISLWIEKGSLKQLIIDMEA LPVSCIEALNQLRALSWQQSDIQIYLLVSDKTPAIAQFIRMAGRFFVLSRRQNLASVR EALLSAAEPRLSESFSRTDWLMIETLAQGASLKEIARQQSVSYHRVVYRLKQLITLLN LPHRQSFLRLIQQLNVTFHDIF" gene complement(781..1092) /locus_tag="D0215_23500" CDS complement(781..1092) /locus_tag="D0215_23500" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_455140.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="diguanylate cyclase" /protein_id="ECV0722577.1" /translation="MVAQGTLLKERITPPHLASSPTRHSYLNSGLLKSEPIVHLSTAQ LIGYEVLTQLSSEHDSEVFFQQLMLMEGIETSEQRSIAFYAGATMGQGYLWPAILPDI Y" gene complement(1254..1850) /gene="fimW" /locus_tag="D0215_23505" CDS complement(1254..1850) /gene="fimW" /locus_tag="D0215_23505" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_459547.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="fimbriae biosynthesis transcriptional regulator FimW" /protein_id="ECV0722578.1" /translation="MLSIAIKEQNSHFEHGLKIIMTRLANQWQQKIDFLPPEEIDNAD IAFLALDDDWFSAGCYQIPMHTQHQLRAIICNKCDKEKLMFRPCLYMLPHIYREDDVE EITRKMILILHKRALRHSVPSGICHYCTTRHFSVTERHLLKLIASGYHLSETAALLSL SEEQTKSLRRSIMRKLHVKTEQQFLKYIRVNLHFLLSK" gene 1806..2042 /locus_tag="D0215_23510" CDS 1806..2042 /locus_tag="D0215_23510" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001523413.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="ECV0722579.1" /translation="MLKVTVLFLNSDTQHKKYPTRQVNHGEILKKLIDFLNTGGLNSH FMRAEMCPGDFLEPGIAPEKTIFVHLGSNQNKSH" gene 2105..2181 /locus_tag="D0215_23515" tRNA 2105..2181 /locus_tag="D0215_23515" /product="tRNA-Arg" /inference="COORDINATES: profile:tRNAscan-SE:1.23" /anticodon=(pos:2139..2141,aa:Arg,seq:tct) gene complement(2140..2328) /locus_tag="D0215_23520" CDS complement(2140..2328) /locus_tag="D0215_23520" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_459548.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="integrase" /protein_id="ECV0722580.1" /translation="MVHRYAHLAPNHLTEHAREIDDIFGDDVPNMSHMENKEEIKKRN ALIYKWRALQDSNLRPTA" gene complement(2440..2735) /locus_tag="D0215_23525" /pseudo CDS complement(2440..2735) /locus_tag="D0215_23525" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000343613.1" /note="frameshifted; incomplete; partial in the middle of a contig; missing start and stop; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="transposase" gene complement(2838..3113) /locus_tag="D0215_23530" CDS complement(2838..3113) /locus_tag="D0215_23530" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000021431.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="ECV0722581.1" /translation="MSIETITWPDVRIIGGVIENLDIYQLTETTAIYSSSTQNCNADN VLTFGGYNGIFFMPLATGTQGGNFDGVSNNVCRLETRFIGPVEEKEK" gene 3851..4213 /locus_tag="D0215_23535" CDS 3851..4213 /locus_tag="D0215_23535" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_455144.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="GtrA family protein" /protein_id="ECV0722582.1" /translation="MLKLFAKYTSIGVLNTLIHWGVFAFCVYGMHTHQALANFSGFVI AVSFSFYANARFTFNASTTTLRYMMYVGFMGTLSAVVGWMADKCSLPPLLTLVTFSAI SLTCGFIYSKFIVFRDAK" BASE COUNT 1156 a 963 c 921 g 1254 t ORIGIN 1 aatttcttaa aaaatcttat tcgccaaaac gttactccgt taaaaaatat cgtggaaagt 61 aacgtttagc tgctggatca gccgaagaaa gctttgcctg tggggaaggt taaggagggt 121 gataagttgt ttaagccggt aaactacacg atgataagat acgctttgct gacgtgctat 181 ttcttttaaa gaggcacctt gcgctaaagt ttcaatcatc aaccagtcag tacggctaaa 241 gctttccgat aagcgaggtt cggcggctga taacaaggct tcgcgtactg aagccagatt 301 ttgtcgtcgt gacagaacaa aaaaacgccc agccatacgg ataaactgag ctatagcggg 361 ggttttatct gataccagca ggtaaatctg gatatcgctt tgttgccaac tgagcgcgcg 421 tagctggtta agcgcctcaa tacaggagac aggtagcgcc tccatatcta taatcagttg 481 tttgagcgac cccttttcaa tccacaaaga aatgtcatct aatgagcgga atgctgcggt 541 acgttttccg gaaaataagt aatgactcag cgaatagccg aggtagttgt cagttgtaat 601 tattgcctga gaaatgatac caaccggcaa ggcataatta agctgttggt ccagtaactc 661 aaggcgatca aatatctgcg gcgttggaga gtgataacgg caggcgcagt ctttggcatt 721 tcttaaacgg cggtgtcttt ccctgcgtgg tacgctgcgc atcctgcttt ttccattgct 781 ctaatatata tctggtaata tggctggcca taaataacct tgtcccatcg ttgcaccagc 841 gtaaaaagca atgcttcgtt gctctgatgt ttcaatgcct tccatcagca ttaactgctg 901 aaaaaaaact tcgctatcat gttctgacga aagttgcgtc aggacctcat agccgattaa 961 ttgcgcagtt gagagatgaa cgattggctc agattttaac aatccgctgt tgagatatga 1021 atggcgtgtt ggtgaagacg ccaggtgtgg gggagttatc ctttccttta ataaagtacc 1081 ctgtgccacc aaacactcct ccaggcattt atgatgcagc catatatttt cgacccctga 1141 atctatcagg atattatggg catcattgtg gcagcgttaa aaaaatgcct gtaggtatcg 1201 ttacttaatt attggtgaga tatttcgtaa gccttgtaaa aagttaagtg agtttactta 1261 ctgagtaaga aatgaaggtt aactctaata tactttaaaa actgctgctc cgttttaaca 1321 tgtaattttc gcataatgct ccggcggagt gactttgtct gctcttcaga aagtgaaagt 1381 aaagcagccg tttcgcttaa atgataaccg ctggcgatca gttttaacag gtgacgttct 1441 gttactgaaa aatgacgagt cgtgcagtag tggcaaatgc cagaagggac gctatgtcga 1501 agcgctcgct tatgtaagat caatatcatt ttccgggtaa tttcttcaac atcatcttcc 1561 cgataaatat gcggcagcat atacagacat ggtctgaaca tgagcttttc tttatcgcat 1621 ttattacaaa taatcgcccg tagctgatgt tgggtatgca taggtatctg gtaacagcct 1681 gcgctgaacc aatcatcatc cagggccagg aaagcgatat cggcattatc tatctcttct 1741 ggcggcagaa agtcaatttt ctgctgccat tgattcgcca gacgcgtcat gatgattttc 1801 aacccatgct caaagtgact gttttgttcc ttaatagcga tactcagcat aaaaaatatc 1861 ctacacggca ggtgaatcat ggtgaaatat taaagaaact tattgatttt ctaaatactg 1921 gcggccttaa ttcccacttt atgcgtgctg agatgtgtcc aggcgatttc ctggaacctg 1981 gcattgcgcc agaaaagacg atattcgtac acttaggcag caaccagaac aaaagccatt 2041 gactcaggag tgcctgaccg tataattctc gcgtttcgtc tacacgaagt cttcacttca 2101 caaggcgccc ttagctcagt tggatagagc aacggccttc taagccgtgg gtcgcaggtt 2161 cgaatcctgc agggcgcgcc acttataaat caacgcgtta cgcttcttta tttcctcctt 2221 attttccata tgggacatat ttgggacatc atcaccaaaa atgtcgtcta tttccctcgc 2281 gtgttccgtt aaatgattag gcgcaaggtg agcatatctg tgaaccattt caatagattt 2341 ccatccccca tttcctaaag cactgacagt ggaactcctg attgaattaa ccagcttgcc 2401 catgtgtgcc taaggccgtg aaagcgaaag tcttctattt ttattttcgc ccagccacat 2461 acccggctgc gctttctggc cttcggtgtt gatacccagc gcgaggaaga cggctttgtt 2521 tatgatgctg tgactttgga tatcaatgtg agcgacacat cggcgtcgta catttctttg 2581 aaggtggcgg agatttcgcg cgtgaccatg cctttgacat acagcgataa aatctggctg 2641 tccatctgtg tgagccgcgt ctggttcttc ttaatcaact gaggtttgaa ggtgttttca 2701 cggtcacgcg gcgtgttcag ttcaatctcg ccatcaccgc aatttacctg tcctcgttat 2761 cggaatgaat atatcaaaaa caggcagata tacaatttaa attacagtct ctcaacaaaa 2821 cgtagatgca ccttgtttta tttttctttc tcttctacag ggccaatgaa acgcgtctcc 2881 aatcgacaga cattattgga aaccccgtca aagttgcccc cttgagttcc tgttgccagc 2941 ggcatgaaga aaatcccgtt atatccacca aacgtgagca cattatcagc attgcaattc 3001 tgtgtggaac tggagtaaat ggctgtagtt tcggttaact ggtagatatc taggttctcg 3061 ataactccgc cgatgattct cacatccggc cacgtgatag tctcaataga caaaaatgat 3121 caggcagtga tatccgtgcc tgtctgtcgt aatatcgcat gaccgccaat ttcggagatg 3181 caacggtgca ctagagagat ttttgatgag taatattccg cgacgggcaa aatacatttt 3241 ttaacgcttt ctgtagcctc aatatactgc ttattctcaa atgtactccc ggcattcggc 3301 atggtgccaa atttagtcgc atctcatggg ccgatgatac atttctacgc ataggtagag 3361 gccactgcaa tagtgtctct ctcatctgtt aatccggttt tatctacacc ctgaaaaacg 3421 cagcgacatt cccctgatga tctgcatgcc agcagtacat aatccccaat agacagtgga 3481 ataaaaatac taaaataaga gtaaatagtt gattataaaa ttattaatct gcgggattcg 3541 aacttggaac cctcgactta gaagtttctg taaccgccgt ttaagccaac aagttatcct 3601 gttatcaatg caaacacatg acccaccttc gagaaacata caaagctttg tatgccccaa 3661 atcaccaggt aatcatcaaa ctcgctgtaa ctcacagcat tttccaatat caacctatcg 3721 attgcaacga tcgattttaa tgtgtgtgat agctgaaagc tatcaaacac tagattattg 3781 atcgtcttta tcgatcaaat caatttgtag tgctacactc cagacctttc cgaatccgct 3841 gattttcata atgttgaagt tattcgctaa gtacacatcg atcggtgttc ttaacacgct 3901 tattcattgg ggcgtatttg ctttttgtgt gtatgggatg catacgcatc aggcgctggc 3961 gaacttttcc ggttttgtta tcgccgtatc gttcagcttc tatgccaatg cgcgcttcac 4021 ctttaacgcc agcaccacca cgcttcgcta catgatgtac gtgggattta tgggaacact 4081 gagcgccgtt gttggctgga tggctgacaa atgttccctg ccgccactcc ttactcttgt 4141 caccttttca gctatcagcc tgacatgcgg attcatttat tcaaagttca ttgtctttag 4201 ggatgcgaaa tgaaagtctc gttagtcgtt ccggtcttca atgaagaagc cacgatacct 4261 attttctata aaacggttcg cgagtttgaa gagc //