LOCUS       NZ_CP064669             4936 bp    DNA     circular CON 12-JAN-2024
DEFINITION  Salmonella sp. SJTUF14154 plasmid p14154C, complete sequence.
ACCESSION   NZ_CP064669
VERSION     NZ_CP064669.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15296096
            Assembly: GCF_015534775.1
KEYWORDS    RefSeq.
SOURCE      Salmonella sp. SJTUF14154
  ORGANISM  Salmonella sp. SJTUF14154
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4936)
  AUTHORS   Zhang,Z., Shi,C. and Shi,X.
  TITLE     Prevalence and Evolution of high drug-resistance Salmonella Indiana
            in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4936)
  AUTHORS   Zhang,Z., Shi,C. and Shi,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUN-2020) MOST-USDA Joint Research Center for Food
            Safety, Shanghai Jiao Tong University, Dongchuan RD800, Shanghai
            200240, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SOAPdenovo v. 2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 24x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/12/2024 03:08:51
            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)                     :: 4,823
            CDSs (total)                      :: 4,705
            Genes (coding)                    :: 4,535
            CDSs (with protein)               :: 4,535
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 63 of 170
            Pseudo Genes (incomplete)         :: 130 of 170
            Pseudo Genes (internal stop)      :: 32 of 170
            Pseudo Genes (multiple problems)  :: 48 of 170
            Pseudo Genes (short protein)      :: 1 of 170
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP064669.1.
            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..4936
                     /organism="Salmonella sp. SJTUF14154"
                     /mol_type="genomic DNA"
                     /strain="SJTUF14154"
                     /isolation_source="Chicken meat"
                     /db_xref="taxon:2745893"
                     /plasmid="p14154C"
                     /geo_loc_name="China:Shandong"
                     /lat_lon="37 N 117 E"
                     /collection_date="2017"
                     /collected_by="Shanghai Jiao Tong University"
     gene            join(4624..4936,1..11)
                     /locus_tag="IVP16_RS23860"
                     /old_locus_tag="IVP16_23860"
     CDS             join(4624..4936,1..11)
                     /locus_tag="IVP16_RS23860"
                     /old_locus_tag="IVP16_23860"
                     /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_000955996.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="IVP16_RS24250"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="IVP16_RS24250"
                     /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            689..1207
                     /locus_tag="IVP16_RS23870"
                     /old_locus_tag="IVP16_23870"
     CDS             689..1207
                     /locus_tag="IVP16_RS23870"
                     /old_locus_tag="IVP16_23870"
                     /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_112016408.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKDAIALFTTSTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQDGRRKFLVLPYGKSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="IVP16_RS23875"
                     /old_locus_tag="IVP16_23875"
     CDS             1214..1447
                     /locus_tag="IVP16_RS23875"
                     /old_locus_tag="IVP16_23875"
                     /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_096987281.1"
                     /translation="MTELETHLLNALKQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSGQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2058..2354)
                     /locus_tag="IVP16_RS23880"
                     /old_locus_tag="IVP16_23880"
     CDS             complement(2058..2354)
                     /locus_tag="IVP16_RS23880"
                     /old_locus_tag="IVP16_23880"
                     /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_138650211.1"
                     /translation="MERKHKGKCPFCNSEMAPEVIEKNTIRRDKCKCTTCGEIIYKCRN
                     IFCNDYAKGGLLYDDELCPPCGEGLLKAVKEFPDKYRAAIQKVVEEKNREKNN"
                     /name="hypothetical protein"
     gene            complement(2429..2584)
                     /locus_tag="IVP16_RS23885"
                     /old_locus_tag="IVP16_23885"
     CDS             complement(2429..2584)
                     /locus_tag="IVP16_RS23885"
                     /old_locus_tag="IVP16_23885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010940654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1508 domain-containing protein"
                     /protein_id="WP_072210546.1"
                     /translation="MNDKWEFYLDNSKEWRWRRTASNGRIVGASSQGYVNKSDCIDNAR
                     RHGYNG"
                     /name="DUF1508 domain-containing protein"
     gene            complement(3551..3709)
                     /locus_tag="IVP16_RS24325"
     CDS             complement(3551..3709)
                     /locus_tag="IVP16_RS24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071777339.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(4368..4559)
                     /locus_tag="IVP16_RS23890"
                     /old_locus_tag="IVP16_23890"
     CDS             complement(4368..4559)
                     /locus_tag="IVP16_RS23890"
                     /old_locus_tag="IVP16_23890"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4206..4290
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          complement(3638..4195)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.821"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1545
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.534"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4592..4935
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.043"
                     /coverage="97.0"
                     /evalue="1.05e-62"
ORIGIN
        1 atgatagtta agtttcatgc caggggaaaa ggtggtggca gtggtccggt tgattacctg
       61 ctggggaggg agcgtaatcg cgaaggcgca acggtgcttc agggtaatcc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtccggtgt tctgtcgttt
      181 gcggagaaag aactgccacc gggaggacgt gaaaaagtga tggcgagttt tgagcgtgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca ccaggacaag
      301 ggacggcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
      361 cagccgtact acgaccgggc agacaggccg agaattgatg cctggcagac gctggttaat
      421 caccattacg ggctgcatga ccccaacgcc ccggagaatc gccggacgct gacactccct
      481 gataacctgc cggaaacgaa acaggcgctt gctgagagcg ttacacgagg cctggaggtg
      541 ctttaccatt ccggagagat aaaaggccgt caggatgtga ttcaggcgct cacagaggtg
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
      661 aggaatatca gactgaaagg agcgttttat gagcaatctt ttacggacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaaa atgctgaacg acgaattcag
      781 caggctcggc gaatctgtaa gcgaggctgt gacctcaaac gagacgaaaa tcaaagacgc
      841 tatagccctg ttcacaacgt cgacagagga atcgctgaaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcacc ggaaggacat gttaaagctg gcagggagtt cgggcatgag
      961 gttgctgggg atagtctttc tcctgtttac cgcgagtggc gggacgctct ggtatctcgg
     1021 cgggaggata cagacgaacc tggaagaaat cagggtacag gaagagacat tgcggaaact
     1081 gaacgcgaag acatggggtg tggagtttgt tcaggacggg agaaggaaat ttctggtcct
     1141 tccgtacggg aaatcagcag aggtgactca ctatcagggg aaggactgga tacaactgac
     1201 ggagtgatac ggaatgacag agctggaaac acatttgctg aacgccttaa agcagctgca
     1261 acaggactat atgcagcggc tgaacgaatg ggagagcgcc ttcgtggaat tgcagaagat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag cgggtcatgc agttgagtca
     1381 gcaggtgcaa cacttgagcg ggcagacaga acgcttgagc cagttataca gcgagaacag
     1441 gagataaggg atgaacggct gatgcaggag cgcgaacatg cattatccct ggagcgggaa
     1501 cgccagctgg aaatacagga acgcacactg gatggtcctt cgttgtcgct gtgatggcga
     1561 aactatgaaa aatggcaggt tcggtggatt ttgacgggct aatgtggtct gcaccatctg
     1621 gttgcatagg tattcatacg gttaaaattt atcaggcgcg atcgcggcag tttttcgggt
     1681 ggtttgttgc catttttacc tgtctgctgc cgtgatcgcg atgaacgcgt tttagcggtg
     1741 cgtacaatta cagggttatg ttaaattgat ggtttgataa gtgttggaaa taattaattc
     1801 cactcataaa tatacaagat atgaaaaaaa tattgttcat atggtagaag agctataggg
     1861 atatttggtt tcaaaatatt ccttttagga aatggattaa ctaaaacagg tactaaaata
     1921 cctgttaaaa ataatgagag agataactct ctgttagggc gtgtgttggg gatatagaaa
     1981 tatttggtat tgcttacgaa atcgattggt tttcatgata attaactaat atagttatat
     2041 ggttttgtgc gctaccatta attattcttt tctctattct tctcttctac aactttttga
     2101 attgctgctc gatacttatc agggaactct tttaccgcct ttaaaagacc ttcaccacat
     2161 ggagggcaca gttcgtcatc gtaaagtaat ccgccttttg cgtagtcatt acagaatata
     2221 tttcggcatt tataaataat ctctccacaa gttgtacatt tacatttatc tctgcggata
     2281 gtgttttttt ctataacttc tggagccatt tcgctattgc aaaaagggca cttacctttg
     2341 tgttttcttt ccatggtatt tttctatttg tttatctctt tgcaattggg attcctgctt
     2401 ggaatcccaa catgagaatc aatttatatt agccgttgta gccatgacga cgtgcgttat
     2461 caatacaatc agatttattg acatatcctt gagatgatgc tccaacaatt cgcccgttgc
     2521 ttgcagttct gcgccagcgc cactcttttg aattatcgag ataaaactcc cacttatcgt
     2581 tcatttaggt ttccttcttc cagttagata tttagtgatg atttgtacca gcaggtaggt
     2641 atcatttcat ttttttttct aataagcgtg ttacaactgt actgacgacg atacttaagg
     2701 ctgttgtccc taatgcgccg atacttctac ctatgttcga catgcatgac gggcataatt
     2761 catcatcata taaatgaccg cccttagcgt aattctcaca tcctggagta cgacatacgt
     2821 aaattattga tttacaatca gaacactcac acttatctcg ccgtatcttg ttttcttgaa
     2881 ttacacgggc attgatttcc tttttacaaa aaggacacac tcctttaggt tttaagtcca
     2941 ttagggttta cctaatagca ctacaactta ttaattttga acgacattta gggcaataat
     3001 caggtgtccc aaatccagct ctactggtcc attcgtggcg gcagtttaag catttagccc
     3061 gatagatgac gatacctgcc ataaaaatcc cctttttatc atacactaat gttgatttat
     3121 tatattctga acataataaa tgtaaagtat actatgtgat aaacgtaatg cattgatttt
     3181 attgatatta aaaatattta ttagagtgct aataatggta ttttttttga tttttttatt
     3241 aaaaacaata tgttgtatat gtgttggtgt cgtttgatta cgttcaataa atgcgtgtat
     3301 caatattaga tatacaaaaa tgaagttaga aggtggctgg gagttttagg agatttgccc
     3361 tccttcagta aaaagatcaa aggatcctct tgagatcctt tttttctgcg cgtaatctgc
     3421 tgcctgtaaa cgaaaaaacc gcctggggag gcggtttagt cgaaggttaa gtcagttggg
     3481 gactgcttaa ccgggtaact ggcttggtgg agcacagata ccaaatactg tccttctagt
     3541 gtagccgcag ttaggccacc acttcaagaa ctcttaatat ctcaatccac cttgtccagt
     3601 taccagtggc tgctgccagt ggcgttaagg cgtgtcttac cgggttggac tcaagacgat
     3661 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     3721 tggagcgaac gacctacacc gaactgagat accaacagcg tgagctatga gaaagcgcca
     3781 cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag
     3841 agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcaggtttc
     3901 gccacctctg acttgagcgt cgatttctgt gatgctcgtc aggggggcgg agcctatgga
     3961 aaaacgccag cggcgtggcc ttttccgggt tcttgttttt tgctcacatg tttcctttgg
     4021 cgttatcccc tgattctgtg gataaccgca ttaccgtctt tgagtgagct gataccgctc
     4081 gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa aagcgcctgg
     4141 acgcgcattt tctccttacg catctgtgcg gcatttcaca cccggcatgg ggcacttttc
     4201 atacaatctg cactgatgcc acatagttaa gccagtatac actccgctag cgctacgtga
     4261 ctggttcagg gcttcgcccc gaaaccccct gacgcgccct gacgggcttg tctgctcccg
     4321 gcatccgctc acagacaagc tgtgaccgtc tccgggagct gtatgtgtca gaggttttca
     4381 ccgtcatccc cgaagcgtgc gaggcagctg cggtaaagct cgtcggcgtg gtcgtgaagt
     4441 gattcacaaa tatcggcctg ttcatctgcg tccagttcgt tgagtttctc cagcagcgtt
     4501 aatgtctggc ttctgataaa gcgggccatg ttaagggcgg ttttttcctg tttagtcact
     4561 gatgcctccg tgtaaggggg atttctgttc atgggggtaa tgataccgat gaaacgagag
     4621 aggatgctca cgatacgggt tactgatgat gaacatgccc ggttactgga acgttgtgag
     4681 ggtaaacaac tggcggtatg gatgcggcgg gtctgcctgg gtgagccggt tgcccgttcc
     4741 gggaagctgc caactttggc tccgccgtta ctgcgtcagc tggccgccat cgggaataac
     4801 ctgaatcaga cagcgaggaa ggtgaacagc gggcagtggt cttccggcga ccgggttcag
     4861 gtggtggccg cactgatggc catcgagaga gagttgcgca gcttacggca ggtcgtcagg
     4921 gaacagggag cgcggg
//
