LOCUS       NZ_CP083732             5430 bp    DNA     circular CON 16-NOV-2023
DEFINITION  Salmonella sp. A29-2 plasmid pA, complete sequence.
ACCESSION   NZ_CP083732
VERSION     NZ_CP083732.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21220878
            Assembly: GCF_020150755.1
KEYWORDS    RefSeq.
SOURCE      Salmonella sp. A29-2
  ORGANISM  Salmonella sp. A29-2
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5430)
  AUTHORS   Liu,Z. and Li,R.
  TITLE     Salmonella drug resistance genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5430)
  AUTHORS   Liu,Z. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-SEP-2021) School of Biology and Pharmaceutical
            Engineering, Wuhan Polytechnic University, Changqinghuayuannanlu8,
            Wuhan, Hubei 430000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 09-AUG-2021
            Assembly Method :: SOAPdenovo v. V2; unicycler v. V3
            Assembly Name                     :: A29-2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 249.64x
            Sequencing Technology             :: Illumina HiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/16/2023 03:02:27
            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)                     :: 4,763
            CDSs (total)                      :: 4,640
            Genes (coding)                    :: 4,506
            CDSs (with protein)               :: 4,506
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 40 of 134
            Pseudo Genes (incomplete)         :: 100 of 134
            Pseudo Genes (internal stop)      :: 22 of 134
            Pseudo Genes (multiple problems)  :: 26 of 134
            Pseudo Genes (short protein)      :: 1 of 134
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083732.1.
            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..5430
                     /organism="Salmonella sp. A29-2"
                     /mol_type="genomic DNA"
                     /strain="A29-2"
                     /isolation_source="market"
                     /host="chicken"
                     /db_xref="taxon:2876620"
                     /plasmid="pA"
                     /geo_loc_name="China"
                     /collection_date="2020-12-20"
     gene            746..1156
                     /locus_tag="K8W53_RS23760"
                     /old_locus_tag="K8W53_23760"
     CDS             746..1156
                     /locus_tag="K8W53_RS23760"
                     /old_locus_tag="K8W53_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            1414..1977
                     /locus_tag="K8W53_RS23765"
                     /old_locus_tag="K8W53_23765"
     CDS             1414..1977
                     /locus_tag="K8W53_RS23765"
                     /old_locus_tag="K8W53_23765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749520.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(2006..2632)
                     /locus_tag="K8W53_RS23770"
                     /old_locus_tag="K8W53_23770"
     CDS             complement(2006..2632)
                     /locus_tag="K8W53_RS23770"
                     /old_locus_tag="K8W53_23770"
                     /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_223149424.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHINDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     gene            complement(2934..3017)
                     /locus_tag="K8W53_RS23935"
     CDS             complement(2934..3017)
                     /locus_tag="K8W53_RS23935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071532987.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHD"
                     /name="replication initiation protein"
     gene            3655..3975
                     /locus_tag="K8W53_RS23775"
                     /old_locus_tag="K8W53_23775"
     CDS             3655..3975
                     /locus_tag="K8W53_RS23775"
                     /old_locus_tag="K8W53_23775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957082.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNTGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGND
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4184..>4618
                     /locus_tag="K8W53_RS23885"
                     /pseudo=""
     CDS             4184..>4618
                     /locus_tag="K8W53_RS23885"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            4653..5138
                     /locus_tag="K8W53_RS23785"
                     /old_locus_tag="K8W53_23785"
     CDS             4653..5138
                     /locus_tag="K8W53_RS23785"
                     /old_locus_tag="K8W53_23785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /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_001749519.1"
                     /translation="MSSLLALAKDLEKQSKAQQQNTCEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEQKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            5142..5354
                     /locus_tag="K8W53_RS23790"
                     /old_locus_tag="K8W53_23790"
     CDS             5142..5354
                     /locus_tag="K8W53_RS23790"
                     /old_locus_tag="K8W53_23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3368..3547
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          complement(2909..3422)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3966..5428
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.057"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtttccgt cagcggagct ataacggtcc gacgctgggc tgactgcgcg catccagtga
       61 caaaccccaa gaagaagggc tcataaattt cccgctaaat acggtcgtga tgaaaagatc
      121 acggctcaag agagggggat ttatgaagat actaaaagcg ctcagtctga tactgcaatg
      181 cgtcaaactg gcaatggatc tgtgggagcg attcggggga aagtggcctt tttagtgctt
      241 tacaccgtat ttatacgcga aaactgctgt cattcacctg gctgcataac catgcagcta
      301 ggtgaaattt atctggcgta aacggggcgg tttaccgggt gctttgctag gggtttcacc
      361 cgacaggcac cgtatttgcg ccgaaccagc ccgaagcggt gcgggcaaga actcttatgt
      421 taaattcatc tcatcggcaa cctatacagg cataaaaatc agtttctata agcggctttc
      481 ttgcacctac ttggtgattt ttttggatgc gctgacgttg ctcgacttta aatcaccata
      541 gaaaaatacc ctttacttac ataaagatcg atctggatgt gtatcttgac gaggttaaat
      601 acgagcaatt gtttttgtat ttaaggtttc ttatcgccgt tttttgcggc tctagaaaaa
      661 tcaatacaaa agatcttgaa agtcacctcg ctccctgggt acacttccgt ataagaactg
      721 atcgatgtct aaaacggatt gtattatggc ttttatctct ctatcgaact tggcagcgaa
      781 gactggaagg ataatccagt cgcagtgtgt tacggccacg caaacaaaaa aaagcacggg
      841 cgctgtcgag ctgggattcc gcttgagcaa gagcgctatg gacgagactg gtattaccat
      901 tggggatcgt gtcgacattc tttacgacaa agaagaaaac cagtggatga ttaagaaaat
      961 tagtgaaggt ggctttggtg tgtctgggca aaaaaacaag cacggcggtt actcatcgtg
     1021 tgctgttaga ttgaccttgc gaccaggttt tcctcgcctt tctgaggatg aagaggacaa
     1081 caagaagcta ctttccgatg attcattcac tcagctaagt gaaggtgtaa tcgtcttcag
     1141 gctggatgat gaataggaag gaccaaaaag gaaaggcaga gttagtgagc gtcgccaaac
     1201 aatcgactaa ctccgccttc tggtcaacac atcactacct ttggaagggt ggagtgttat
     1261 gggcggcatt atgttcataa acttgcattc taataaagaa aaaatcgttt cttttgaggg
     1321 atgtgaacac gacattttct attctgatag gtgcgatgct attggctttg gtctcttaag
     1381 tttatgtttt taaaaacata tgaggctata catatgcacg ctttatcaat actaccttca
     1441 gttgcccgcg ctaacctggc aactaaattc tcgtctcatt tgaaggtgat cgagctcttc
     1501 aacacgatgc aggattccca agttgttgtc ttgtcatcac tgatcgaagg ccatcacctc
     1561 accagttctg gtaacagtgt caaagccgac tttgaggtca ctcgcttacc ggcgattatc
     1621 gagatgttag agaaaaaata ttttttccct attcgtcatc taaatgtatc tgttaaatct
     1681 gtaactacag gaaggatgac tggacaaact gtctatttca tagagcctga acacatcgag
     1741 caacttctcg ctgatcctga gcttgtgttt gctaatcagg aaaggagcct cttctttcgt
     1801 tctctcgaaa aagaagggaa aaatctcggc aagcttatcg agaaaaaagg tagtgtttct
     1861 caagccgtct taagccttct acatcacgcc tacaaagata aacctctttc tgacgagatg
     1921 tggaaggaga tagaagataa gttcacccat atgctggatg aattgagcgc ggcgtaaagg
     1981 caagggcggt cgttagaccg cctttttagt cttctaaacc taattctttg tgatagtttt
     2041 tcagcgtaga gtaacgatag tttctgagta tgttttcatc tttcttgacg ttcgcttcta
     2101 tgtatctgtt tacgaatttg ttgaaatctt cttgtatttt ttctttgtta tcattgatat
     2161 gggtaaattc aggagttggt atcttatagg ctcgcgatac atactcttct ttcttaatta
     2221 gcaacgcttt ggtgtaatcc agtcctttct taacaccttc tgatcgctcc gaaacgaatc
     2281 caaatttatg gtttaaatgg cttcgtaagg gtatcccgaa caccaatccg ttgagatcaa
     2341 taactacgat tccgtagcct cttacttttc catcattact gccgtcgaga gcctcttgta
     2401 ggcctttgtt atcagcataa aactggtctg taagggttct taactgtatg taatcctgtt
     2461 tgctcatttt tgatgtccat tggcattttc ctgtaaccaa tgtacaaaaa aagcaaagcc
     2521 ctctgtaaga gagggctttg cttttctttc gttgagtctt ggatttttta cgtgtggcga
     2581 actctaccgc acatctttct ttggaagctt gtttgtttaa cgtggggctc attcctaccg
     2641 ccacttctag atttacttat atcaaaaatt atatgtgaag tcaatttcgt agctgttctt
     2701 gactggactt actttgccag cgtaatcttc tcctgaaacg aaaaaaccac cctggcaggt
     2761 ggtttttcga aggttattta atcctggcag attatctaac cgtggtaaca gtcttgtgcg
     2821 agacgtgtca ccaaatccgt ccttccagtg tagcctcagt aaggccacca cttcaagaac
     2881 tctcaataca tctctcgcac atcatgttta ccagtggccg ttgccaatgg cgattagtcg
     2941 tgtctttccg ggttggactc aagtcgatag ttaccggaaa aggcgcagcg gtcggactga
     3001 acggggggtt cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc
     3061 aggcgtggaa tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc
     3121 aggaacagga gagcgcacga gggagccacc agggggaaac gcctggtatc tttatagtcc
     3181 tgtcgggttt cgccaccact gatttgagcg tcagatttcg tgatgcttgt caggggggcg
     3241 gagcctatgg aaaaacggca gcgccgcatc cttttcttgc cctgtttgtc atgccgtgtg
     3301 cctttgctct tatccgtgtg caggtaacgc ccgccgcagc cgaacggcag gagcggaagc
     3361 gaccgagtga gcgaggaggc gtaatatcac cgcaacctcc atgttctccc gtacgccctg
     3421 cagctgcatt ttcccctgcc acatgaagca cttttataaa gtgttactcc gccgtaacat
     3481 attaagccag tatacactcc gctagcgcta cgtgactggt tcagggctgc gccccgaaac
     3541 ccgctaaaag ccactgacgc gcctgcggct tgtccaacac cgtgccgacc gggaaacatt
     3601 tcccgcccgt cccggtgtta tcaggaggct actctggcag acaaacgcaa caagatgctc
     3661 acgatgtggg tgacggaaga cgaacaccgg cggctgctcg agcggtgcga cggcaagcag
     3721 ctggcggcgt ggatgcgtca gacctgcctc gatgagaagc cggcgcgtgc cggcagactg
     3781 ccgtcgatat cgccggcgct gctgcgccag cttgccggta tgggtaataa cctgaaccag
     3841 atcgcccgga aagtgaatac cggtggtgcc ggtcatgacc gggtgcagat cgtggccgcc
     3901 ctgatggcaa tcgacgcggg actggagcgg ctgcggcatg cggtgctgga aaaagggggg
     3961 aatgatgatc gttaaattcc atccccgggg gcgcggtggt ggtgccggtc cggtggatta
     4021 cctgctggga aaagaccggc agcgcgaggg ggcgaccgtg ctgcagggaa agccggagga
     4081 agtccgggag cttatcgatg cctcgccgta tgcgaaaaag tacacctccg gcgtactgtc
     4141 gttcgcggag gctgagctgc cgcccgggca gcgggagcag atcatggcca gctttgagcg
     4201 ggttctgatg cccgggctcg ataaagacca gtacagcatt ctgtgggtgg agcacaccga
     4261 caaggggcgg ctggagctga atttcctgat ccccaacaca gagctgctga ccgggaaacg
     4321 cctgcagccg tattacgatc gcgccgaccg gccgcgcatc gatgcctggc agaccgtggt
     4381 gaacggcaga ctggggctgc atgatccaaa cgccccgaag aaccggcggt tactggtcac
     4441 gccgtccgca ctgccggaaa cgaagctgga agccgctcag gcgattacac ggggtttgct
     4501 ggccttagcc tcatccgggg cgctcaaaac gcgcgaggac gtcacagggg cgctcactgc
     4561 ggcaggtttt gaggtggtcc gcaccacaaa gaacagtatc agcattgccg acccggacgg
     4621 ggggcgaaac atccgactga agggagccat ttatgagcag tcttttagcg ctggcgaagg
     4681 acttggaaaa gcaatcgaaa gcgcagcagc agaatacctg cgagatgctg aaagccgcat
     4741 tcagcgagca cgagaagtct gtaaaagcgg aactgagcgc aagcgcgaag agaatcagcg
     4801 acgccatcag cgcccacgag cagggtatga ccgcggcgat gcagtcgaac cggctgagcg
     4861 tgctgcgtat ggttggccgg acgtggctga ccatcaccct ggtctcagta ctgctgatcg
     4921 ccacgagcgg gagcattctg tggtggcagg ggcagcagat caccgggaat taccagacta
     4981 tccgggcgca ggagcggacg caggccatgc tgtcggagaa gaaccacggc gtgcagctgt
     5041 cgctctgtgg ggaacagaaa ctgtcctgcg tcaaagtgaa cccgaaagcg ggagcttacg
     5101 gggaggaagg gaactggatg gtactggaga ggaaatagcc catgacggaa ctggaaaaac
     5161 agttgctgac cgcattagag cagctacatc aggactactc gcaaaggctg gacgagtggg
     5221 agagcgcctt cgcggaatgg cagaagatgt ctggtcttat gcaacgggag aacgcggcgc
     5281 tgaacgagcg cgtcacgcgc ttgagtcagc aggtggcgaa cttgagcagg cagttacagc
     5341 gtttgagcca gtagtgcagc ggcatgaaat ggcggtggcc gccgaacggg catacgagca
     5401 gcgacagcat gaaaaagagc tggcagaacc
//
