LOCUS AAIEQN010000130 3304 bp DNA linear BCT 26-JUL-2019 DEFINITION Salmonella enterica subsp. enterica serovar Muenchen strain 301730 SAMN11046516-rid7307993.denovo.130, whole genome shotgun sequence. ACCESSION AAIEQN010000130 AAIEQN010000000 VERSION AAIEQN010000130.1 DBLINK BioProject: PRJNA248792 BioSample: SAMN11046516 Sequence Read Archive: SRR8661092 KEYWORDS WGS; GMI. SOURCE Salmonella enterica subsp. enterica serovar Muenchen ORGANISM Salmonella enterica subsp. enterica serovar Muenchen Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella. REFERENCE 1 (bases 1 to 3304) AUTHORS Ashton,P.M., Dallman,T., Nair,S., De Pinna,E., Peters,T. and Grant,K. TITLE Direct Submission JOURNAL Submitted (04-MAR-2019) Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom 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 :: 04-MAR-2019 Assembly Method :: SKESA v. 2.2 Assembly Name :: PDT000472831.1 Long Assembly Name :: NCBI Pathogen Detection Assembly PDT000472831.1 Genome Coverage :: 90x Sequencing Technology :: ILLUMINA ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Date :: 03/04/2019 05:39:02 Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Provider :: NCBI Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Annotation Software revision :: 4.7 Genes (total) :: 5,331 CDSs (total) :: 5,249 Genes (coding) :: 5,109 CDSs (with protein) :: 5,109 Genes (RNA) :: 82 rRNAs :: 2, 5 (16S, 23S) partial rRNAs :: 2, 5 (16S, 23S) tRNAs :: 63 ncRNAs :: 12 Pseudo Genes (total) :: 140 CDSs (without protein) :: 140 Pseudo Genes (ambiguous residues) :: 0 of 140 Pseudo Genes (frameshifted) :: 69 of 140 Pseudo Genes (incomplete) :: 63 of 140 Pseudo Genes (internal stop) :: 36 of 140 Pseudo Genes (multiple problems) :: 27 of 140 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..3304 /organism="Salmonella enterica subsp. enterica serovar Muenchen" /mol_type="genomic DNA" /submitter_seqid="SAMN11046516-rid7307993.denovo.130" /strain="301730" /serovar="Muenchen" /host="Homo sapiens" /sub_species="enterica" /db_xref="taxon:596" /geo_loc_name="United Kingdom: United Kingdom" /collection_date="Sep-2016" /collected_by="PHE" gene 12..494 /locus_tag="E0Y79_25245" CDS 12..494 /locus_tag="E0Y79_25245" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_005154726.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="baseplate assembly protein" /protein_id="ECD4200930.1" /translation="MDTVRKCQTAGLKLIAGEKKENVEHLEPYGFTSAAQNGAEAVVL FPGGDRSHGVAVVVADRRFRLKGLARGEVALYDDQGQSVTLTRAGIVVNGGGKPVIFT NATKARFEMPIESTGDIRDNCDSSGKTMAEMRTTYNGHTHKENGDGGGITDKPGQPMS " gene 499..912 /locus_tag="E0Y79_25250" CDS 499..912 /locus_tag="E0Y79_25250" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000605050.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="ECD4200931.1" /translation="MILYVNGIRNDATASLDLLTRAVVISLFTWRRAERDDRTPQPYG WWGDTWPAVQNDRIGSRLYLLKRRKLTNKTPQDAREYMQQALAWMTDDGVAARIDVTS ERTGTDTLAAGVTIYQRDGVIHNITFDDIWSELNG" gene 905..1984 /locus_tag="E0Y79_25255" CDS 905..1984 /locus_tag="E0Y79_25255" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_000785580.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="baseplate J/gp47 family protein" /protein_id="ECD4200932.1" /translation="MADSQFARPELPQLIATIRSDLLTRFQQDVVLRRMDAEVYSRVQ AAAVHTLYGYIDYLARNMLPDMCDEDWLYRHASIKRCPRKNAVSAKGFARWDGIAGRP EIPAGTQIQRDDQVTFTTLQTVKASGGLLRVPVIADVAGTAGNTDDGTALRLGTPITG IPSTGYADTLTGGADTEELETWRARVMERYYWIPQGGADPDYVIWAKEVAGITRAWTF RHYKGTGTVGVMVATSNPVNPAPGDDLVKAVRDHILPLAPVAGGGLFVFAATEKSIPV TVALAKDTPEIRTAIIAELNALMLRDGAPSGKIYVSRISEAISLATGEVAHQLRVPAA DVVLGKTELPVLGNITWATYTGENG" gene 1987..2574 /locus_tag="E0Y79_25260" CDS 1987..2574 /locus_tag="E0Y79_25260" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001207831.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="DUF2313 domain-containing protein" /protein_id="ECD4200933.1" /translation="MALQDEYTQLLYHLLPEGPAWDGENPLIEGLAPSLNRVHQRADE LMAEIDPARTTELIDRYEQLYGLPDSCAPEGVQTLQQRQQRLDAKANVAGGINERFYR EQLDALGYTAATIEQFQNLDSTPDPEWGEFWRYYWRVNIPADANISWQTCTSTCDSAI RTWGDTVAECVIDKLCPSHTVVVFAYPEGKENAQN" gene 2780..>3304 /locus_tag="E0Y79_25265" CDS 2780..>3304 /locus_tag="E0Y79_25265" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_001699730.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phage tail protein" /protein_id="ECD4200934.1" /translation="MDEQVKTRLEKNQNGADIPNKPLFLQNVGLGETINLAAGALQKS QNGGDIPDKKQFARTIGAVTSTTITLGESGWFKIATVVMPQATSTAVIKLYGGAGFNA GSPEQAAISELVLRAGNGSPVGITATLWRRSPAAANEVAWVNTSGDTYDIYINIGQYA YWLIAQYDYTGNANV" BASE COUNT 818 a 793 c 950 g 743 t ORIGIN 1 tcattaccgc gattgatacc gtcagaaaat gccagactgc cggactgaaa cttattgccg 61 gtgaaaaaaa agaaaatgtg gagcatcttg aaccttacgg tttcacttct gcagcacaga 121 atggcgcaga agcggtggta ttgtttcccg gcggtgaccg ttcgcacgga gtggctgtgg 181 ttgtggctga ccgccgcttc agactgaaag ggctggcgcg cggggaagtc gcgctatatg 241 acgatcaggg gcagtcggtc acattaaccc gtgccggaat agtggtaaat ggcggcggaa 301 agccagttat tttcacgaat gccactaaag cacgttttga aatgccgatc gaatccactg 361 gcgatatcag ggacaactgt gacagcagtg gaaaaacgat ggctgaaatg cgcacgacct 421 ataacggtca tacccataaa gaaaatggcg atggcggcgg tataaccgat aagcctggcc 481 aacccatgag ctgacatcat gatcctttat gttaatggaa tccgtaatga tgccacggct 541 tcgctcgacc ttctgacgcg ggcagtggtg atttctcttt ttacctggcg ccgggcggag 601 cgggatgaca ggaccccaca gccatacggc tggtgggggg acacctggcc tgctgttcag 661 aatgaccgca tcggttcccg cctctacctg ctgaaacgcc gcaaactcac caataaaacg 721 ccgcaggatg cccgtgaata catgcagcag gcgctggcgt ggatgacaga cgatggcgtg 781 gcggcacgta ttgatgtgac atctgaacgc acaggaacag ataccctggc agctggcgtg 841 acgatatatc agcgggacgg ggtaattcac aatattacat tcgatgatat atggagcgaa 901 cttaatggct gacagtcaat ttgcacgtcc tgaacttcct cagttgattg ctaccattcg 961 cagcgattta ctgacccgtt ttcagcagga tgttgtgtta cgtcgcatgg atgccgaggt 1021 ttacagccgg gtacaggctg ctgccgtaca tacgctgtat ggttatatcg attatctggc 1081 ccggaatatg ctgcctgata tgtgtgatga ggactggctt taccgtcacg cgagtattaa 1141 gcgttgtccc aggaaaaatg ccgtatctgc gaagggattt gcacgctggg atggtattgc 1201 cggaaggccg gagatccccg cgggtacaca gattcagcgg gatgatcagg ttacattcac 1261 gaccctgcag acggtgaaag cttccggcgg cctgttacgt gtgccggtta ttgctgatgt 1321 ggcgggaact gccggtaata ctgacgatgg tacggcgtta cgccttggta cgccgattac 1381 tggtattcct tctacaggtt acgctgacac tctgaccggg ggggctgata cagaggagct 1441 tgaaacgtgg cgcgcgcgcg tcatggagcg ctattactgg ataccacagg ggggcgctga 1501 tcctgattac gtcatctggg caaaggaagt cgcaggaata acccgtgcgt ggacattccg 1561 ccattataag gggaccggca ccgttggtgt gatggtggct accagtaacc cggttaatcc 1621 ggctcctggc gacgatctcg ttaaggctgt acgtgaccat attttgccgc tggcacctgt 1681 tgctggcggc ggactctttg ttttcgctgc cactgaaaaa agcattccgg taacagtcgc 1741 actggccaaa gataccccgg aaattcgtac tgccattatt gcggagctaa atgcgctgat 1801 gctacgtgat ggcgcgccgt ccggaaaaat ttatgtttcg cgaatcagcg aggcgataag 1861 cctggcgacc ggggaagtgg cacatcagct gcgtgtgccg gcggcagatg tggtactggg 1921 aaaaactgaa cttcctgtcc tggggaatat aacctgggcc acctataccg gggagaacgg 1981 ataactatgg cattacagga cgaatatacg cagttacttt atcaccttct gccggaaggg 2041 cctgcctggg acggagaaaa tccactgatt gaagggctgg cgccgtcgct gaaccgggta 2101 catcagagag cggatgaact gatggctgaa attgacccgg ccagaactac ggaactcata 2161 gaccgttatg aacagctgta tggcctgcct gattcctgtg caccggaagg cgtgcagaca 2221 ttacagcagc gccagcaacg tctggatgca aaggcgaatg ttgccggtgg tataaacgag 2281 aggttttatc gggaacagct tgatgcgctg gggtataccg ctgccaccat tgagcagttt 2341 cagaatctcg acagcacacc cgatcctgaa tggggggaat tctggcgtta ctactggcgt 2401 gtgaatattc cggctgatgc gaacatcagc tggcagacct gtacaagcac ctgcgactct 2461 gcgatcagaa cgtggggcga tactgttgct gaatgtgtga ttgataagct ttgtccgtca 2521 catacggttg ttgtttttgc ttatccggaa ggaaaagaga atgcacagaa ttgatacgcc 2581 caccgcgcaa aaagataaat ttggtcaggg aaaaaacgga tttacgaatg gtgatcccgc 2641 cacgggccgc cgcgcaacgg atctcaacag tgatatgtgg gatgcagtcc aggaagaggt 2701 ctgtactgtt attgaagccg ccggcatacc actcagtaaa ggcgaacata cgcagcttca 2761 cgccgccatt ggcaggctga tcgatgaaca ggttaaaacc cgtcttgaaa aaaatcagaa 2821 tggcgcggac atcccgaata agccgctgtt tctccagaac gttggtttag gagaaacgat 2881 aaatctcgct gcaggggccc tgcaaaaatc gcagaacggc ggcgatattc ctgacaaaaa 2941 acaatttgcg agaaccatcg gtgcggtaac gtcaaccacc attacacttg gcgaatcagg 3001 ctggttcaaa atcgccacgg ttgtaatgcc gcaggctaca tcaactgcgg tgattaaact 3061 gtacggtggg gcggggttta acgctggttc acctgaacag gcggcaatca gcgaactggt 3121 attgcgtgcc ggtaatggtt cacctgttgg aataactgcc acgttgtgga gacgctcgcc 3181 tgctgctgct aacgaggtcg catgggttaa tacatcaggc gacacctacg atatttatat 3241 taatatcggc cagtatgcgt actggttaat tgcgcaatat gattacaccg gtaatgcaaa 3301 tgtc //