LOCUS       NZ_CP126182             4066 bp    DNA     circular CON 24-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,12:i:- strain BL661
            plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP126182
VERSION     NZ_CP126182.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32643670
            Assembly: GCF_030517155.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 1,4,12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 1,4,12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4066)
  AUTHORS   Lopez Garcia,Ad.V., AbuOun,M. and Anjum,M.F.
  TITLE     Pathogen genomics and phage-based solutions to accurately identify
            and control Salmonella dissemination in poultry flocks
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4066)
  AUTHORS   Lopez Garcia,Ad.V., AbuOun,M. and Anjum,M.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JAN-2023) Bacteriology, Animal and Plant Health
            Agency, Woodham Lane, Weybridge, Surrey KT153NB, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 105.88x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/22/2023 16:47:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,018
            CDSs (total)                      :: 4,898
            Genes (coding)                    :: 4,741
            CDSs (with protein)               :: 4,741
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 157
            CDSs (without protein)            :: 157
            Pseudo Genes (ambiguous residues) :: 0 of 157
            Pseudo Genes (frameshifted)       :: 56 of 157
            Pseudo Genes (incomplete)         :: 104 of 157
            Pseudo Genes (internal stop)      :: 27 of 157
            Pseudo Genes (multiple problems)  :: 29 of 157
            Pseudo Genes (short protein)      :: 1 of 157
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP126182.1.
            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..4066
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,12:i:-"
                     /mol_type="genomic DNA"
                     /strain="BL661"
                     /serovar="1,4,12:i:-"
                     /isolation_source="Poultry"
                     /sub_species="enterica"
                     /db_xref="taxon:2801390"
                     /plasmid="unnamed3"
                     /geo_loc_name="Thailand"
                     /collection_date="2019"
     gene            complement(join(4025..4066,1..666))
                     /locus_tag="PGC29_RS25070"
                     /old_locus_tag="PGC29_25070"
     CDS             complement(join(4025..4066,1..666))
                     /locus_tag="PGC29_RS25070"
                     /old_locus_tag="PGC29_25070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1197..1451)
                     /gene="mobC"
                     /locus_tag="PGC29_RS25075"
                     /old_locus_tag="PGC29_25075"
     CDS             complement(1197..1451)
                     /gene="mobC"
                     /locus_tag="PGC29_RS25075"
                     /old_locus_tag="PGC29_25075"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            1630..3777
                     /gene="mobQ"
                     /locus_tag="PGC29_RS25080"
                     /old_locus_tag="PGC29_25080"
     CDS             1630..3777
                     /gene="mobQ"
                     /locus_tag="PGC29_RS25080"
                     /old_locus_tag="PGC29_25080"
                     /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_124770306.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATVRRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(1453..1629)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          1630..1988
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.611"
                     /coverage="100.0"
                     /evalue="1.82e-180"
     Typing          complement(2..666)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1544..3774
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcagggct acaaccgtgc gccccttttt gatcgtctca accgttacag ccaggtcgct
       61 ttttttgttc agttcgtcaa cacagggttt tattagatcc ctgtttaacg ttttgaaatc
      121 tttatattta ccatcaagca tcagtgatga tttaaaatca tcgagggcga taatacgttc
      181 cccagtactg cggaattgct ggagaatttc gtatattctt atgctgtaac ttcttgataa
      241 attagaaata tttttaatga cgactctggt gaattgcccc ttcaactgtg tcagataagg
      301 cattaccgcg tcagaaaaag tgatttgtgc tttcccctct cccctcgcgt actgtgcccg
      361 atactgaatc cagcggaact cctcgcgctt ctcgtcgtcc ttgagaatga tcgacctgtc
      421 ccacaaacga tcgatcgctt cctgtagctg aacctcggca tttttccgcc ccatatcagg
      481 gaatgaatca aaatattccg cagctgtaat ggtcattgtc ttttgcaatt caggtgaagc
      541 tacgtcagta ccggagttaa gtcggcttat gcagagcaat aagaaacgct gttcttgtaa
      601 agttagcttg taactggcct caaccagcgc attggactta taggctatca gagggtttga
      661 tgtcatttta accaccaggc caaagatgag gtgagataaa aacctatcac ctttagcatt
      721 ggtgagcaat tatattttca ccccccattt tcctgtgaat attaccttaa atctcctcac
      781 ctttacctta aattacctca cccaagcacc ttaaattata tcacctttac cttaaatcat
      841 atcacctata gcgttgtaac attttgtttt ctataaggaa tttcgaccct aaaacaagta
      901 ttaaaaacaa gatcttaaaa acaagatcta aaaacttaac ggcgagcctg tggataactt
      961 ggggtgctga aaataaaaat ccaataaaaa caatgtgttg caaaaatcag gattgaagat
     1021 tccgaatacc cccccctcca accctgtgga aatccagtat tcatgcgggt tcagcgcata
     1081 tcacctgtcg aaaaaccgtg cgtatgtgct caacatggcg actgattcac ttccgcttcc
     1141 tcgcccactc actcgctaac gctcggtcgc tgggctgcgg cgagcggacg atacaatcac
     1201 tgctctggca gcgcctccag ctcgttaatc agcggcagta ttcgcgtcac atcagcctgc
     1261 cgtgtcacct ctgccttcag gaactggagt aaccaggctc gcaactgcac ttcctccggc
     1321 tttctgacct ttgccagcaa tgctgcaccc acaatgacct tctgcgctgt gtccaggctc
     1381 cggctcttcg ccttcaggcg ctgtaatctc gcctcagcat cagcaatctt ctgttcgagc
     1441 gttctgctca tgatgtaact ccatgcgcga tgaaaaatcg cattttagcg cgtcactggt
     1501 agtttaaaaa ctgagctggc ataatgcacg gcaaatcacg aagtgcgcac ttatacaatc
     1561 tccactccgt ttcgattgtg tgcgccctgc ggggctgaaa gaaaaccaca aaaaggcatt
     1621 acggcagaaa tggcgattta tcatctcagc atgaaaatca tctccagaaa cagcggctac
     1681 agcgccgttg cttctgctgc ctatcgttct ggttcactga tgcttgatga gcgtaccgga
     1741 ctgactcacg actacacccg caaaagcggt gtggctgagg ctgtgattct gacccccgcg
     1801 acagcccctg cctggtgtac gaaccgtgcc gaactctgga atgccgttga gaaggccgaa
     1861 cgccggaaga actcacaact tgcgcgggaa attgaactcg ccatccccca cgaactgccg
     1921 caggatgccg cacgggaaac cgttctcgcc tttgtcagag aaaactttgt cagtcagggc
     1981 atgattgctg atgtggcgtt ccatcacatg gataaaacaa atccccatgc gcacatcatg
     2041 ctgaccacga gagctgtcgg acctgctgga ttcggtggaa aggtcaggga ctggaacgac
     2101 cggacacatg ccgagacgtg gcgggcatca tgggctgacc atgcaaacag ggcactggcg
     2161 aacgccggtt atcaggaaga gatagaccat cgttcatacg agcgacaggg gcttgagaaa
     2221 acgcctggta ttcacctcgg aaagtctgcc tgtgcgatgg aaacacgagg tatcgaaaca
     2281 gaacgcggcg aacagaatcg tctgattaac agacttaacc tggaaataca gatttcccgt
     2341 accgaactca ggaacggagg gctgacagag cctgcccgcc gtgtggctga ccttctgaat
     2401 atcgggcttc ctgacaacgc aacttcgtac acactacgtg acatcatcga agcgttgccg
     2461 aaggacagta actcggcatg gaaactcacc agtaatgcca tgtcgatgat ggcagatatg
     2521 caggcgacgc gcagacgctg ggaagagctg aacaccgaac gaaaggaagc gatgagccat
     2581 gctgccagcc tgaaaaaatc atcgccgttt tcgtccggtt tttcccgtat tcccctgatg
     2641 caatgggcgg caccggaata ccgtagtgag cagggaaaaa tccagtctct gagccagcaa
     2701 atggaaaaat tgcgacagca ttaccggaag gtggagaaac aggacattcc cgcgagtcag
     2761 atggcatttg aaaaacagtg gcagcagtgg ggggaatccg gccttgcagc tctcagagcc
     2821 cagttgctta aacgtgaaga ggaattgcgc cggaaggaac aggaagatac tgaacgtagt
     2881 cgcgcggagc agctcaggaa aaatgacaat gccgttatgg attcaggggt actgagcgca
     2941 gtcgttacgg ggtatggcga ggcccccatg cctggtaacg gggaaatgac ctgttacctt
     3001 ctgcttcata accggaacgg agaatatacg ctctggggta acgagctgga gaaataccgc
     3061 accagaatct ttgagcgtgt tgatttaatg cgtgacagga gtggttatat ctgtgaccga
     3121 agcgaaatcg gccaacgtcc gccactgcaa cgtgtttatt cctctgcgac ctttgagcaa
     3181 ctgctgacgc aggtttgcca gacatggccg caacataccc gcaatctccg ccagccgaag
     3241 acatggccgg agtctttctg tcttggagaa gaccgccagc cagccatgcc atcactggca
     3301 gcaaggaagg tggattttac gcagggacgt ctgccaccga cgctgatgcc ggtcatgagt
     3361 tctgtcgacc gggaaacccg ccagcttcag cttttgctgg tcatgggcgt ggatgactct
     3421 ctgggcggtg ttgtccggct taatggtacg ctgtatcccg cgtttgccgt tccctcagcc
     3481 gataacagcc agctggtcat cagtgcacta accgataagg ggttacggta tgcagggtat
     3541 ggtgttgccg taaatcacga tgcagacagc cacatatcac ctgcaccaga actgatgcag
     3601 tttcatctga aaacccgtga ggcaccgctt tttgctgccg tcaacacacc agaaaaacag
     3661 ccggatcatc tgttccgctc gctgggtttt aatcgtacct gggacgaatg gcggcgcgag
     3721 gaagatgcac gaacacacgc caccgtgagg agacatgatc gcggttggtc acagtgaatg
     3781 tgaacaatat tttgttttgt gtaacatcgt gttatgttcg ccgatgttca tcgacaggga
     3841 tgaatgcaag aagcacactc acatagcgca aacatagttt tgtttttccg cccccaaaaa
     3901 ttggggattc tttttttgct gcatcagagc gtttttgacg caacttttca cttcaatagt
     3961 accttcgcat tcctgacaca agaaaaacgc gacagtgagc gttttaggtg ccttaaaatc
     4021 gattctagat cgtcatcttg atctgtttgt cttccttgaa gcgaaa
//
