LOCUS       NC_019136               5687 bp    DNA     circular CON 14-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Derby plasmid pSD5.6,
            complete sequence.
ACCESSION   NC_019136
VERSION     NC_019136.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14225865
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Derby
  ORGANISM  Salmonella enterica subsp. enterica serovar Derby
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5687)
  AUTHORS   Bleicher,A., Schofl,G., Rodicio Mdel,R. and Saluz,H.P.
  TITLE     The plasmidome of a Salmonella enterica serovar Derby isolated from
            pork meat
  JOURNAL   Plasmid 69 (3), 202-210 (2013)
   PUBMED   23333216
REFERENCE   2  (bases 1 to 5687)
  AUTHORS   Bleicher,A. and Schofl,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-AUG-2012) Cell and Molecular Biology, Leibniz
            Institute for Natural Product Research and Infection Biology,
            Beutenbergstrasse 11a, Jena, Thuringia D-07745, Germany
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009960265.1-RS_2024_03_14
            Annotation Date                   :: 03/14/2024 03:00:33
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 8
            CDSs (total)                      :: 8
            Genes (coding)                    :: 7
            CDSs (with protein)               :: 7
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JX566769.1.
            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..5687
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /serovar="Derby"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pSD5.6"
     gene            1..1131
                     /locus_tag="HTB65_RS00005"
                     /old_locus_tag="pSD56_001"
     CDS             1..1131
                     /locus_tag="HTB65_RS00005"
                     /old_locus_tag="pSD56_001"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_000216732.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(1515..1748)
                     /locus_tag="HTB65_RS00010"
     CDS             complement(1515..1748)
                     /locus_tag="HTB65_RS00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1755..2273)
                     /locus_tag="HTB65_RS00015"
     CDS             complement(1755..2273)
                     /locus_tag="HTB65_RS00015"
                     /function="essential for mobilization of the plasmid"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_031942530.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2311..3009)
                     /locus_tag="HTB65_RS00055"
                     /pseudo=""
     CDS             complement(<2311..3009)
                     /locus_tag="HTB65_RS00055"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2951..3274)
                     /locus_tag="HTB65_RS00025"
                     /old_locus_tag="pSD56_003"
     CDS             complement(2951..3274)
                     /locus_tag="HTB65_RS00025"
                     /old_locus_tag="pSD56_003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3339..3530
                     /locus_tag="HTB65_RS00030"
                     /old_locus_tag="pSD56_004"
     CDS             3339..3530
                     /locus_tag="HTB65_RS00030"
                     /old_locus_tag="pSD56_004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165974.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3682..3978)
                     /locus_tag="HTB65_RS00050"
     CDS             complement(3682..3978)
                     /locus_tag="HTB65_RS00050"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_237141859.1"
                     /translation="MLVRGGGAYGKNASGAAFFALCLFAHMFFPALSPDSVDNRIAVFE
                     QADSARRSRTTERSESVSEEAEKRLDVHFLLTHLCGISHPAWCTFHTMRPDAE"
                     /name="hypothetical protein"
     gene            complement(4544..5611)
                     /locus_tag="HTB65_RS00040"
                     /old_locus_tag="pSD56_006"
     CDS             complement(4544..5611)
                     /locus_tag="HTB65_RS00040"
                     /old_locus_tag="pSD56_006"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="WP_015059941.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPILE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKDIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     Typing          complement(3616..3695)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.67e-34"
     Typing          3727..4270
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.343"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1412..2961)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.374"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgacagtta aaaacaatta cttaaacaga ggttatttgg taacctctac gactcaggcg
       61 aaaaaaatag caaagttgca cctagagaaa ttagacttag ctgataaatt ttcctttggg
      121 ttacctgaag tcgatgatcg gtaccatgta tggcgtgtac cattagtagc gacaggccac
      181 aggattggtg aaatagttat aaattcaaaa acgtcaacta ttgattataa gaaaagttcg
      241 aagtctccat ttcttattaa gaaagcaatg gaggttgtcc ataccccaaa aaaggtaaaa
      301 aaagaaaaaa aaatcatatc aaagtcacca ttaaataaca tgttactaca aggcaactgc
      361 gcggagacct tgaaaaaatt acctgatgaa tcagtgaact tagtattcac atcaccgcca
      421 tattacaatg ccaaaccaga gtattccgaa tatcatacat atgatgaata cctctctcta
      481 ttgcgttcag taataaaaga gtgccataga gttttaagcg aaggtcgttt tttcgtcatc
      541 aatgtctcgc ccgttttaat aagaagggcg tcacggaatg aagcatcaaa aagaatagct
      601 gttccttttg acttgcacag gttatttata gaagaaggct atgaattcat agatgatata
      661 cattgggtta aaccagaagg agctggctgg gctttaggta gaggccgtcg attcgcagct
      721 gaccgcaatc cgttgcaata taaaccagta ccagtaactg agtacattct tgtttacaga
      781 aaaaaaactg ataaattaat agattggaac ataagaaacc atcatagcaa agaggatgtt
      841 tttgactcaa aaatcggcga cgattatgaa aagacaaacc tatggaaaat aaatccatct
      901 cgtaacagaa aacatcctgc tacatttcca tacggtctgg cagaaagagt tataaaatac
      961 tattctttca aaaatgatgt tattttagat ccttttgctg gatcgggaac aacagcaaaa
     1021 gcagcaattg atttaggcag aagatttgtg atgtgtgaga tatcaaagca gtatattgat
     1081 ctgatcatag aaggaaccat gctaggtggt gatttaaaaa tcataaatta atcaaacttt
     1141 actgtggtaa aagccgcctt aaggcggctt atttacgcgt caacatcagc cacattgtcg
     1201 aatttaccat aatcccttaa ttgtacgcac cgccaaaacg cgttcagcgc gatcacagca
     1261 gcagacaggt aaaaatggca acaaaccacc cgaaaaactg ccgcaatcgc gcctgataaa
     1321 ttttaaccgc atgaatacct atgcaaccag atggtacaga ccacattagc ctgtcttaat
     1381 ccacttaacc tgccattttt catggtttca ccatcccagc gaagggccat ccagcgtgcg
     1441 ttcctgtatt tccggctgac gctcccgttc cagggataac acatgttcgc gctcctgtat
     1501 cagccgttcc tctcttatct ccagttctcg ctgtataact ggctcaagcg ttctgtctgc
     1561 tcgctcaagt gctgcacctg ctgactcaac tgcatgaccc gctcgttcag catcgcgttg
     1621 tcccgttgcg taagcgaaaa catcttctgc aattccacga aggcgctctc ccattcgctc
     1681 agccgctgca tatagtcctg ttgcagctgc tctaaggcgt tcagcaaatg tgtttccagc
     1741 tctgtcactc tgtgtcactc cttcagatgt acccactctt tcccctgaaa gggaatcacc
     1801 tccgctgatt tcccgtacgg aaggacaagg aatttcctgt tcccgtcctg cacaaactcc
     1861 acgccccatg tcttcgcgtt cagtttctgc aatgtctctt cctgcttcct gatttcttcc
     1921 aggttcgcct gtatcctccc tccaagatac cagagcgtcc cgccactcgc tgtaaacagg
     1981 agaaagacta tccccagtaa catcatgccc gtattccctg ccagctttaa cacgtccttc
     2041 ctgtgctgca tcatcgcctc tttcacccct tcccggtgtt tttccagcga tttctctgtc
     2101 gaggctgtga acagggctat agcgtctctg attttcgtct cgtttgaggt cacagcctcg
     2161 ctgacagact cgccgagcct cctgaactcg ttgttcagca ttttctctgt agattcggct
     2221 ctctctttca gctttttctc gaactccgcg cccgtctgta aaagattgct cataaaatgc
     2281 tcctttcagc ctgatattcc tcccgccgtt cgggtctgca atgctgatac tgcttcgcgt
     2341 caccctgacc acttcaatcc ctgcctccgt gagcgcctga atcacatcct gacggccttt
     2401 tatctccccg acatgataaa gagcgtctat cccgcgtgtg acgctctctg caagcgcctg
     2461 tttcgttttc ggcaggttat cagggagagt cagtatccgg cggttctccg gggcgttggg
     2521 gtcatgcagc ccgtaatggt gattaaccag cgtctgccag gcatcaattc tcggcctgtc
     2581 tgcccggtcg tagtacggct ggaggcgttt tccgctctgt agctccatgt tcggaatgac
     2641 aaaattcagc tcaagccgtc ccttgtcctg gtgctccacc cacaggatgc tgtactgatt
     2701 tttttcgaga ccgggcatca gtacacgctc aaagctcgcc atcacttttt cacgtcctcc
     2761 cggcggcagc tccttctccg cgaacgacag aacacctgac gtgtatttct tcgcaaatgg
     2821 cgtggcatcg atgagttccc ggacttcttc cggattaccc tgaagcaccg ttgccccttc
     2881 ccggttacgc tcccttccca gcaggtaatc aaccggacca ctgccaccac cttttcccct
     2941 ggcatgaaat ttaactatca tcccgcgtcc cctgttccct gacggccaga cgcagccggc
     3001 gcagctcatc cccgatggcc atcagtgcgg ccactacctg aacccggtca ccggaagacc
     3061 actgtccgct gttcaccttc ctcgctgtct gattcaggtt attcccgatg gcggccagct
     3121 gacgcagtaa cggcggtgcc agtgtcggca gcttcccgga acgggcaacc ggctcaccca
     3181 ggcagacccg ccgcatccat accgccagtt gtttaccctc acagcgttcc agtaaccggg
     3241 catgttcatc atcagtaacc cgtatcgtga gcatcctctc gcgtttcatc ggtatcatta
     3301 cccccatgaa cagaaatccc ccttacacgg aggcatcagt gactaaacag gaaaaaaccg
     3361 cccttaacat ggcccgtttc atcagaggcc agacattaac gctgctggag aaacttaacg
     3421 aactggacgc agatgaacag gcagatatct gtgaatcgct tcacgaccac gccgatgagc
     3481 tttaccgcag ctgcctcgca cgtttcgggg atgacggtga aaacctctga cacatgcagc
     3541 tcccggaaac ggtcacagct tgtctgtgag cggatgccgg gagccgacaa gcccgtcagg
     3601 acgcgtcagc gggttttagc gggtgtcggg gcgcagccct gacccagtca cgtagcgata
     3661 gcggagtgta tactggctta cttattcggc atcagggcgc attgtatgaa aagtgcacca
     3721 tgccgggtgt gaaatgccgc acagatgcgt aaggagaaaa tgcacgtcca gacgcttttc
     3781 cgcttcctcg ctcactgact cgctgcgctc ggtcgttcga ctgcggcgag cggagtctgc
     3841 ttgctcaaaa acggcaatac ggttatccac agaatcaggg gataaggccg gaaagaacat
     3901 gtgagcaaaa agacaaaggg caaaaaaagc cgcgccgctg gcgttttttc cataggctcc
     3961 gccccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca
     4021 ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg
     4081 accctgccgc ttaccggata cctctccgcc tttctccctt cgggaagcgt ggcgctttct
     4141 catagctcac gctgttggta tctcggctcg gtgtaggtcg ttcgctccaa gctgggctgt
     4201 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag
     4261 tccaacccgg aaagacacgt aaaaacgcca ctggcagcag ccattggtaa ccgggttagc
     4321 agagcgagat ttataagttg gtaacagagt tcttgaagta tcagcctgat tctggctaca
     4381 ctagaagaac aagttttggt ggtctgcgct ctgcttaagc cagattacct ggttagataa
     4441 tctgccagga ttagctaacc tttgaaaaac cacctgccag ggtggttttt ctttatgtag
     4501 agattatgct tttaataagc acgcagtcaa ggattacaat ctcttataat ttaatgtatt
     4561 tttccagatc tacattctct aatgcatcag atataaaaga ctgtatgtct ttaagttgag
     4621 gtttatcctc taaaagatca tctacattca gtttcgaact aatataggaa gagacctttg
     4681 caacccaata cgggtcactc atcgcaacaa ctttaccatc aatctcttca gccatattaa
     4741 ctattctact tctatcacca ataacgtcaa caataaccat tgtgcttata ttatgcatca
     4801 ctccgccaat atcatccatt cgtctaaatc tagatacttt atccaaactt atttctgtgt
     4861 tacccctacc aataaaacca atgtcaaccc taatcgcctt cccattaaaa acaagagtag
     4921 catcagactc cctgtcatca gctcttgttg aaagagtaaa acatttagca tttaaccctt
     4981 cttcaatttt ttctttatat tcaaaaccca ttattgtaaa taaagaaccg agtattagct
     5041 tttcaaaata tttaccatga agagatttct cagatcccct aatagttaaa gtttgcgaac
     5101 caagagataa aataatatag caaaaatctt ctaaagacac cttttgccca ccaatagata
     5161 tctctccaat tttatcttca tacccgtttt ttattttaag tatttcttct tgcgtcctta
     5221 aagcaagtct atcaaaacca tccccatgct catctcttaa aacattttgg gtctgtttat
     5281 ttgtcatcat aaccatccac tcgagaatag gttgattaga cttaacataa gacttgttcg
     5341 ataatgcatt ttttgcatag agataaagct gctttggcgt tatcccttct ttcattttat
     5401 ccacaaaaaa gtcaaaaaaa gagagattgc tttctaacaa tctagtacga gttagtattt
     5461 cagtgaattc gcgaacattt ttacctgtta aaacatcata aacaaccttt ttaaaaacat
     5521 ccgttccgaa cttatctaaa acatcatttt ttgaaatttt cgccaacgct atgagttcgt
     5581 tagggaaaca atttttatcc ttgaaattca tatcctcacc atggacatag taaaaatgag
     5641 atgctaagat agcaggttgt atggtaacag atcgatagtt aggaaaa
//
