LOCUS       NZ_CP044963             4072 bp    DNA     circular CON 17-NOV-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014881 plasmid pPNCS014881.2, complete sequence.
ACCESSION   NZ_CP044963
VERSION     NZ_CP044963.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333171
            Assembly: GCF_009017315.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Complete genome sequences of Canadian Typhimurium and I
            1,4,[5],12:i:-
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-OCT-2019) Public Health Agency of Canada, National
            Microbiology Laboratory at Guelph, 110 Stone Road West, Guelph,
            Ontario N1G3W4, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: APR-2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/17/2023 03:18:00
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,086
            CDSs (total)                      :: 4,968
            Genes (coding)                    :: 4,840
            CDSs (with protein)               :: 4,840
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 41 of 128
            Pseudo Genes (incomplete)         :: 101 of 128
            Pseudo Genes (internal stop)      :: 20 of 128
            Pseudo Genes (multiple problems)  :: 31 of 128
            Pseudo Genes (short protein)      :: 1 of 128
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP044963.1.
            Bacteria and source DNA available from 16-7746.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4072
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014881"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="pPNCS014881.2"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2016-10-01"
                     /collected_by="BC Centre for Disease Control"
                     /note="I 1,4,[5],12:i:-"
     gene            1..702
                     /locus_tag="E5O18_RS25640"
                     /old_locus_tag="E5O18_25640"
     CDS             1..702
                     /locus_tag="E5O18_RS25640"
                     /old_locus_tag="E5O18_25640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(960..3107)
                     /gene="mobQ"
                     /locus_tag="E5O18_RS25645"
                     /old_locus_tag="E5O18_25645"
     CDS             complement(960..3107)
                     /gene="mobQ"
                     /locus_tag="E5O18_RS25645"
                     /old_locus_tag="E5O18_25645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3286..3540
                     /gene="mobC"
                     /locus_tag="E5O18_RS25650"
                     /old_locus_tag="E5O18_25650"
     CDS             3286..3540
                     /gene="mobC"
                     /locus_tag="E5O18_RS25650"
                     /old_locus_tag="E5O18_25650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2750..3108)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3109..3285
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2..702
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(964..3194)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcagatc tgatagctta caaatcaaac gcccttatcg aggcaagcta caagctcact
       61 ttgcaggaac agcgcttcct gctggtctgt atcagccgcc taaaatccgg agaagattcc
      121 ccttcgccgg atgaacaaaa aaccatgacc atcacggctg cagagtttca tgatgccttt
      181 cctgacatgg gacggcagca cgctgaagct aggctcaagg aagcgataga tcgcctctgg
      241 gacaggtcag taatcatcaa gaacgaggaa aaacgagaag agttccgctg ggtgcagtac
      301 cgggcgcagt atttcaaagg tgaggcgaaa gtagatatca ccttctccga tgccatcatg
      361 ccgtatctga cacagctcaa ggggcagttt acgcgggtag tcgtgaagaa cgtctccagc
      421 ctttccagca cctacagcat ccgcatttac gagctgctcc agcagttccg cagcaccggt
      481 gacagaacga tagctatcga tgatttccga accatgcttg ccgttgaaga taaatatcaa
      541 caattcaaag acttgaataa gatgataatc aagccagcca tcgccgaact gaacgaaaaa
      601 agcgatctgg ttgtaactgt tgagacgatc aaaaaggggc gcacggttgt agccctgcat
      661 tttcgcttca aggaagacaa acagatcaag atgacgatct aaaatcgatt ttaaggcacc
      721 taaaacgctc cctgctgcgt tttttttgtg ttagtagtgc gaaggtacta ttgaagtgaa
      781 aaattgcgtc aaaaacgctc tgatgcagcg aaaaaagacc ccccaatttt tgggggcgga
      841 aaaacaaaac tatgcttgcg ttatgtgagt gtgcttcttg cattcatccc tgtcgatgaa
      901 catcgaagaa catcgacgaa cataacacga tgttaaacaa aacaaaatat tgttcacatt
      961 cactgtgacc aaccgcgatc atgtctcctc tcggtggtgt gtgttcgtgc atcttcctcg
     1021 cgctgccatt cctcccaggt acgattaaaa cccagcgagc ggaacagatg atccggctgt
     1081 ttttctggtg tgttgacggc agcaaaaagc ggtgcctcac gggttttcag atgaaactgc
     1141 atcagttctg gtgcaggtga tatgtggctg tctgcatcgt gatttacggc aacaccatac
     1201 cctgcatacc gtaacccctt atcggtcagc gcactgatga ccagatgcct gttatcggct
     1261 gagggaacgg caaacgcggg atacagcgta ccattaagcc ggataacacc gcccagagag
     1321 tcatccacgc ccatgaccag caaaagctga agctggcggg tttcccggtc gacagaactc
     1381 atgaccggca tcagcgtcgg tggcagacgt ccctgcataa aatccacctt ccttgccgct
     1441 ggtgatggca tggctggctg gcggtcttct ccaagacaga aagactccgg ccatgtcttc
     1501 ggctggcgga gattgcgggt atgttgcggc catgtctggc aaacctgcgt cagcagttgc
     1561 tcaaaggttg cagaggaata aacacgttgc agtggcggac gttggccgat ttcgcttcgg
     1621 tcacagatat aaccactcct gtcacgcatt aaatcaacac tctcaaagat tctggtgcgg
     1681 tatttctcca gctcgttccc ccagagcgta tattctccgt tccggttgtg aagcagaagg
     1741 taacaggtca tttccccgtt accaggcatg ggagcctcgc cataccccgt aacgactgct
     1801 ctcagcaccc ctgaatccat aacggcattg tcatttttcc tgagctgctc cgcgcgacta
     1861 cgttcagtat cttcctgttc cttccggcgc aattcctctt cacgtttaag caactgggct
     1921 ctgagagctg caaggccgga ttccccccac tgctgccact gtttttcaaa tgccatctga
     1981 ctcgcgggaa tgtcctgttt ctccaccttc cggtaatgct gtcgtaattt ttccatttgc
     2041 tggctcagag actggatttt tccctgctca ctacggtatt ccggtgccgc ccattgcatc
     2101 aggggaatac gggaaaaacc ggacgaaaac ggcgatgatt ttttcaggct ggcagcatgg
     2161 ctcatcgctt cctttcgttc ggtgttcagc tcttcccagc gtctgcgcgt cgcctgcata
     2221 tctgccatca tcgacatggc attactggtg agtttccatg ccgagttact gtccttcggc
     2281 aacgcttcga taatgtcacg tagtgtgtac gaagttgcgt tgtcaggaag cccgatattc
     2341 agaaggtcag ccacacggcg ggcaggctct gtcagccctc cgttcctgag ttcggtgcgg
     2401 gaaatctgta tttccaggtt aagcctgtta atcagacgat tctgttcgcc gcgttctgtt
     2461 tcgataccgc gtgtttccat cgcacaggca gactttccga ggtgaatacc aggcgttttc
     2521 tcaagcccct gtcgctcgta tgaacgatgg tctatctctt cctgataacc ggcgttcgcc
     2581 agtgccctgt ttgcatggtc agcccatgat gcccgccacg tctcggcatg tgtccggtcg
     2641 ttccagtccc tgacctttcc gctgaaccca gcaggtccga tagccctcgt ggtcagcatg
     2701 atgtgcgcat ggggatttgt tttatccatg tgatggaacg ccacatcagc aatcatgccc
     2761 tgactgacaa agttttctct gacaaaggcg agaacggttt cccgtgcggc atcctgcggc
     2821 agttcgtggg ggatggcgag ttcaatttcc cgcgcaagtt gtgagttctt ccggcgttcg
     2881 gccttctcaa cggcattcca gagttcggca cggttcgtac accaggcagg ggcggtggcg
     2941 ggggtcagaa tcacagcctc agccacaccg cttttgcggg tgtagtcgtg agtcagtccg
     3001 gtacgctcat caagcatcag tgaaccggaa cgataggcag cggaagctac ggcgctgtag
     3061 ccgctgcttc tggagataat tttcatgctg agatgataaa tcgccatttc tgccgtaatg
     3121 cctttttgta gttttctttc agccccgcag ggcgcacaca atcgaaacgg agtggagatt
     3181 gtataagtgc gcacttcgtg atttgccgtg cattatgcca gctcagtttt taaactacca
     3241 gtgacgcgct aaaatgcgat ttttcatcgc gcacggagtt acatcatgag cagaacgctc
     3301 gaacagaaga ttgctgatgc tgaggcgaga ttacagcgcc tgaaggcgaa gagccggagc
     3361 ctggacacag cgcagaaggt tgttgtgggt gctgcattgc tggcaaaggt cagaaagccg
     3421 gaggaggtgc agttgcgtgc ctggttactc cagttcctga aggcagaggt gacacgacag
     3481 gctgatgtga cgcgcatact gccgctgatt aacgagctgg aggcgctgcc agaacagtga
     3541 ttgtatcgtc cgctcgccgc agccccagcg accgaacgta gtgagcgagt gggcgaggaa
     3601 gcggaagtga atcagtcgcc aggttgagca catacgcacg gtttttcggc aggtgatatg
     3661 cgctgaaccc gcatgaatac tgggtttcca cagggttgga gggggtgtat tcgaaacttg
     3721 caattctgct ttattgcaac gcattgtttt tattggtttt ttgttttcag caccccaagt
     3781 tatccacagg ctcgccgtta agtttttaag atcttatttt tagatctttt tttttaaaac
     3841 ctttttaggt cttgtaacac catgatttta aagatgttct ggcaagataa gtggagcttt
     3901 tgggggtgaa aggtggagct tttgggggtg aaaggtggag cttttggggg tgaaaggtgg
     3961 agcttttggg ggtgtaatcc acagaaaaag ggggttgcaa aaaaaaaact tccacccata
     4021 tgataagtgg cgtacagtaa aaaaacgcca ccaatagcaa cgagcaagcg aa
//
