LOCUS       NZ_CP126181             4074 bp    DNA     circular CON 24-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,12:i:- strain BL661
            plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP126181
VERSION     NZ_CP126181.1
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 4074)
  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  JOURNAL   Unpublished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 4074)
  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
            CP126181.1.
            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..4074
                     /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="unnamed2"
                     /geo_loc_name="Thailand"
                     /collection_date="2019"
     gene            complement(join(4033..4074,1..660))
                     /locus_tag="PGC29_RS25055"
                     /old_locus_tag="PGC29_25055"
     CDS             complement(join(4033..4074,1..660))
                     /locus_tag="PGC29_RS25055"
                     /old_locus_tag="PGC29_25055"
                     /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_001281396.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1193..1447)
                     /gene="mobC"
                     /locus_tag="PGC29_RS25060"
                     /old_locus_tag="PGC29_25060"
     CDS             complement(1193..1447)
                     /gene="mobC"
                     /locus_tag="PGC29_RS25060"
                     /old_locus_tag="PGC29_25060"
                     /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            1626..3791
                     /gene="mobQ"
                     /locus_tag="PGC29_RS25065"
                     /old_locus_tag="PGC29_25065"
     CDS             1626..3791
                     /gene="mobQ"
                     /locus_tag="PGC29_RS25065"
                     /old_locus_tag="PGC29_25065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /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_302510898.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQKEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRAQL
                     LKREDELRRKELEDTERSRAERRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFESVDLIRDRSGYICDRSEIGQHPPLQRIYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     Typing          complement(1449..1625)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          1626..1984
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.611"
                     /coverage="100.0"
                     /evalue="1.82e-180"
     Typing          complement(3..660)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.393"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1540..3782
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.861"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgcagggct acaaccgtgc gccccttttt gatcgtctca accgttacaa ccagatcgct
       61 tttttcgttc agttcggcga tggctggctt gattatcatc ttattcaagt ctttgaattg
      121 ttgatattta tcttcaacgg caagcatggt tcggaaatca tcgatagcta tcgttctgtc
      181 accggtgctg cggaactgct ggagcagctc gtaaatgcgg atgctgtagg tgctggagag
      241 gctggagacg ttcttcacga ctacccgcgt aaactgcccc ttgagctgtg tcagatacgg
      301 catgatggca tcggagaagg tgatctctac tttcgcctca cctttgaaat actgcgcccg
      361 gtactgcacc cagcggaact cttctcgttt ttcctcgttc ttgatgatta ctgacctgtc
      421 ccagaggcga tctatcgctt ccttgagcct agcttcagcg tgctgccgtc ccatgtcagg
      481 aaaggcatca tgaaactctg cagccgtgat ggtcatggtt ttttgttcat ccggcgaagg
      541 ggaatcttct ccggatttca ggcggctgat acagaccagc aggaagcgct gttcctgcaa
      601 agtgagcttg tagcttgcct cgataagggc gtttgatttg taagctatca gatctgacat
      661 ttcgcttgct cgttgctatt ggtggcgttt ttttactgta cgccacctat catattggtg
      721 gaagtttttt ttttgcaacc ccttttttct gtggattaca cccccaaaag ctccacttat
      781 cacccccaaa agctccacct atcaccccca aaagctccac ctatcacccc caaaagctcc
      841 acctatctcg ccagaacacc tttaaaatca tgtggttaca agacctaaaa aggttttaaa
      901 aaaaaagatc taaaaataag atcttaaaaa cttaacggcg agcctgtgga taacttgggg
      961 tgctgaaaat aaaaatccaa taaaaacaat gtgttgcaaa aaaccaggat tgaagattcc
     1021 gaatacaccc cctccaaccc tgtggaaatc cagtattcat gcgggttcag cgcatatcac
     1081 ctgtcgaaaa accgtgcgta tgtgctcaac atggcgactg attcacttcc gcttcctcgc
     1141 ccactcgctc gctaacgctc ggtcgctggg ctgcggcgag cggacgatac aatcactgct
     1201 ctggcagcgc ctccagctcg ttaatcagcg gcagtattcg cgtcacatca gcctgccgtg
     1261 tcacctctgc cttcaggaac tggagtaacc aggctcgcaa ctgcacttcc tccggctttc
     1321 tgacctttgc cagcaatgct gcacccacaa tgaccttctg cgctgtgtcc aggctccggc
     1381 tcttcgcctt caggcgctgt aatctcgcct cagcatcagc aatcttctgt tcgagcgttc
     1441 tgctcatgat gtaactccat gcgcgatgaa aaatcgcatt ttagcgcgtc actggtagtt
     1501 taaaaactga gctggcataa tgcacggcaa atcacgaagt gcgcacttat acaatctcca
     1561 ctccgtttcg attgtgtgcg ccctgcgggg ctgaaagaaa accacaaaaa ggcattacgg
     1621 cagaaatggc gatttatcat ctcagcatga aaatcatctc cagaaacagc ggctacagcg
     1681 ccgttgcttc tgctgcctat cgttctggtt cactgatgct tgatgagcgt accggactga
     1741 ctcacgacta cacccgcaaa agcggtgtgg ctgaggctgt gattctgacc cccgcgacag
     1801 cccctgcctg gtgtacgaac cgtgccgaac tctggaatgc cgttgagaag gccgaacgcc
     1861 ggaagaactc acaacttgcg cgggaaattg aactcgccat cccccacgaa ctgccgcagg
     1921 atgccgcacg ggaaaccgtt ctcgcctttg tcagagaaaa ctttgtcagt cagggcatga
     1981 ttgctgatgt ggcgttccat cacatggata aaacaaatcc ccatgcgcac attatgctga
     2041 ccacgagggc tgtcggacct gcggggttcg gcggaaaggt cagggactgg aacgaccgga
     2101 cacatgccga gacgtggcgt gcatcatggg ctgaccatgc aaacagggca ctggcgaacg
     2161 ccggttatca gaaagagata gaccatcgtt catacgagcg acaggggctt gagaaaacgc
     2221 cgggtattca cctcggaaag tctgcctgtg cgatggaaac acgcggtatc gaaacagaac
     2281 gcggcgaaca gaatcgtctg attaacaggc ttaacctgga aatacagatt tcccgcaccg
     2341 aactcaggaa cagcgggctg acagagcctg cccgccgtgt ggctgacctt ctgaatatcg
     2401 ggcttcctga caacgcaact tcgtacacac tacgtgacat catcgaagcg ttgccgaagg
     2461 acagtaacgc ggcatggaaa ctcaccagta acgccatgtc gatgatggca gatatgcagg
     2521 cgacgcgcag acgctgggaa gagctgaaca ccgaacgaaa ggaagcgatg agccatgctg
     2581 ccagcctgaa aaaatcatcg ccgttttcgt ccggtttttc ccgtattccc ctgatgcaat
     2641 gggctgcacc ggaataccgt agtgagcagg gaaaaatcca gtctctgagc cagcaaatgg
     2701 aaaaattgcg acagcattac cggaaggtgg agaaacagga cattcccgcg agtcagacgg
     2761 catttgaaaa acagtggcag cagtgggggg aatccggcct tgcagctctc agagcccagt
     2821 tgcttaaacg tgaagatgaa ttacgccgga aggagctgga ggatacagaa cgtagtcgcg
     2881 cggagcgacg agcggaacag ctcaggaaaa atgacaatgc cgttatggat tcaggggtgc
     2941 tgagagcagt cgttacgggg tatggcgagg ctcccatgcc tggtaacggg gaaatgactt
     3001 gttaccttct gcttcacaac cggaacggag aatacacgct ctgggggaac gagctggaga
     3061 aataccgcac caggatcttt gagagtgttg atttaatacg tgacaggagt ggttatatct
     3121 gtgaccgaag cgaaatcggt caacatccac cactgcaacg tatttattcc tctgcgacct
     3181 ttgagcaact tctgacgcag gtttgccaga catggccgca acatacccgc aatctccgcc
     3241 agccgaagac atggccggag tctttctgtc ttggagaaga ccgccagcca gccatgccat
     3301 cactggcagc aaggaaggtg gattttacgc agggacgtct gccaccgacg ctgatgccgg
     3361 tcatgagttc tgtcgaccgg gaaacccgcc agcttcagct tttgctggtc atgggcgtgg
     3421 atgactctct gggcggtgtt gtccggctta atggtacgct gtatcccgcg tttgccgttc
     3481 cctcagccga taacagccag ctggttatca gtgcactgac cgataagggg ttacggtatg
     3541 cagggtatgg tgttgccgta aatcatgatg cagacagcca catatcacct gcaccggaac
     3601 ttatggagtt tcatctgaaa acccgtgagg caccgctttt tgctgtcgtc aacacaccag
     3661 aaaaacagcc ggatcatctg ttccgctcgc tgggtttcaa tcgtacctgg gacgaatggc
     3721 ggcgcgagga agatgcacga acacacgcca ccgagaggag acctgatcgc ggttggtcac
     3781 agggaatgtg aacaatattt tgttttgttt aacatcgtgt tatgttcgtc gatgttcatc
     3841 gacagggatg aatgcaagaa gcacactcac atagcgcaaa catagttttg tttttccgcc
     3901 cccaaaaatt gggggttctt tttttgctgc atcagagcgt ttttgacgca acttttcact
     3961 tcaatagtac cttcgcattc ctgacacaag aaaaacgcga cagtgagcgt tttaggtgcc
     4021 ttaaaatcga ttctagatcg tcatcttgat ctgtttgtct tccttgaagc gaaa
//
