LOCUS       NZ_CP048622             2683 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia stuartii strain MF1 plasmid pMF1A, complete sequence.
ACCESSION   NZ_CP048622
VERSION     NZ_CP048622.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14048635
            Assembly: GCF_010669105.1
KEYWORDS    RefSeq.
SOURCE      Providencia stuartii
  ORGANISM  Providencia stuartii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Cao,G.
  TITLE     Complete genome of Providencia stuartii MF1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Cao,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-FEB-2020) Shandong Medicinal Biotechnology Center,
            Shandong First Medical University, 18877 Jinshi Road, Jinan 250062,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SOAPdenovo v. Jan-2020
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 283.0x
            Sequencing Technology             :: BGISEQ
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_010669105.1-RS_2024_03_11
            Annotation Date                   :: 03/11/2024 12:01:58
            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)                     :: 4,258
            CDSs (total)                      :: 4,152
            Genes (coding)                    :: 4,029
            CDSs (with protein)               :: 4,029
            Genes (RNA)                       :: 106
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 51 of 123
            Pseudo Genes (incomplete)         :: 93 of 123
            Pseudo Genes (internal stop)      :: 34 of 123
            Pseudo Genes (multiple problems)  :: 44 of 123
            CRISPR Arrays                     :: 6
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP048622.1.
            Bacteria and source DNA available from DNA is available from Dr.
            Guangxiang Cao.
            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..2683
                     /organism="Providencia stuartii"
                     /mol_type="genomic DNA"
                     /strain="MF1"
                     /isolation_source="wastewater from pig manure"
                     /db_xref="taxon:588"
                     /plasmid="pMF1A"
                     /geo_loc_name="China:Shandong"
                     /collection_date="2018-08-24"
     gene            complement(479..1123)
                     /locus_tag="G3A48_RS21225"
                     /old_locus_tag="G3A48_21230"
     CDS             complement(479..1123)
                     /locus_tag="G3A48_RS21225"
                     /old_locus_tag="G3A48_21230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032495680.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrD1"
                     /protein_id="WP_012634451.1"
                     /translation="MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSF
                     YDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNM
                     ITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSS
                     FDWSLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrD1"
     gene            complement(2084..2524)
                     /locus_tag="G3A48_RS21230"
                     /old_locus_tag="G3A48_21235"
     CDS             complement(2084..2524)
                     /locus_tag="G3A48_RS21230"
                     /old_locus_tag="G3A48_21235"
                     /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_015063446.1"
                     /translation="MSQLFRLASPEDYEYIEELNLWELSFDKRPVQGVRCEDPVIGAEK
                     YNQGREKFKALASRHKKHWKPNGLTFSELIRWAIECGTPEQCQLVLALYHCTNDDDYQA
                     MGIQLSRSIDNANVSPIIFFTGKNQRLLGDISMLKQLEEKVR"
                     /name="hypothetical protein"
     ARG             complement(483..1123)
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(1218..1373)
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 cacagggctc tggtactcta aatcttgtgc attcgttgct cagattagac gtcgcaatcc
       61 aatcttagca acgtgagagg cgcttgtcac gttctcatta aataccagcc aacgacatta
      121 acccaaatgc accacttgat tgactcggac ttagcccggt ctccgaaagg ataaacaggc
      181 aaattgtggt agtaaaacgt accggaaaac gaaattccgg ctctacctcc gaatcacgct
      241 gcggtatcga aagattacag tgcgtacctg ataagagcac caatcaacgg actagggatt
      301 tcttggattg cgaagtgtcg aaagaagccc aacctaacca aacttagcca gattaacgag
      361 ctaagagacc atgacccaat aactgatcat ggagaaaagc aaagacaaga tgaagatgtc
      421 gcttcgctcc gttttgatta gtaccacatt ggggcattag gcgtttttta cctagatttt
      481 atcggtgaac aataacacct aaactctcaa caagctgaag cgcctgctct ccatccaact
      541 tcactccatc taaattaatt cgccttgcat caagctcgcc aagcgcccca cccgttaaat
      601 cacaaccagt aaaatcagcc aaagaccaat caaacgatga aaactcccca caagaaagat
      661 cggagccacg aaacacggcg ccagttatca cagtgccatt ccagcgattt tcccacagtt
      721 cgcacttttc taatatgact ctagaaaaat tagcgtaact aagatttgtc ttggttatat
      781 aagcactaca aaaccatgac cttgtagtta tcatattcat aaaattagcc cctcgaaaat
      841 cagctccttg agctaaacac tcactaattt caagacctaa ggcgctaatg tttttaaaat
      901 tactcattga taaatcgcag cttttaaagc tagcgttttt tagtttggct ctattaaaat
      961 cacacccttc caagctattc ctgtcgtaaa aactacaatc aacaaattca gtatcagtta
     1021 aatcaacccc tgaaaaatca caatttgaaa aggcaatatt tttaactcta ttccccgtaa
     1081 attgatctcg tgaaaacttt tcattgataa agtgcttttc catacatgct acacctggtt
     1141 atttatacag tgcaatcatt gtacattaat ttgaacaacc ttaaactcta gctaaaattg
     1201 attcatacaa tcccttttat gttaaacggg cgagttagtt agcaaaaacc tcccgttcat
     1261 ccccattaaa gcccctcgaa acgattttaa gacacgatca ccctataaaa cacccaaatc
     1321 tacgctgaaa gtttagaacg gttttgcggg cttctgagtg cgtttttaac atcgtgcaaa
     1381 ctgacaagta aaacgatgcg aaatcgctga aagtcacaaa cttgttttgt ggcaagaagc
     1441 gatttgacca accgagtaaa acgagggcgg taggcttttt gtttttatcc tgatgagcgt
     1501 ccagcgaaga aagggaaaaa cagggggagc cgaaacgaaa tgacacgccc cagcgatggc
     1561 aagtgaaccc cagtgaacgt gtttcgtttt gggggcaaag ccccccgtca agcgaagcgt
     1621 ctgaccacca catttttgag cgaccaaata caggggcgaa aaaagggggt ggtcagacga
     1681 acgcagtgag tttgacgggc ttgggtgaat ggtttttttc gcaggcgtcc agccgaagaa
     1741 aatagccaga gggcggagcc ttatgtcatt cattttcgtc cagaaaatga gtggcattga
     1801 tactgaaagt atcatggggt gcaagttagt aaaactatga ttctacccat tatttcaccc
     1861 gttattctgc ccgttatacc taaattgggt gcaataacgg gtaaagtaat aggtagaata
     1921 acaggtggat taatgggtaa gaaataacac aacgtcatct tgtgtctatc tattattctg
     1981 tatcttattc tatgtattat tctacctatt acagacgaaa tagataaaat aagagataga
     2041 ataatagata ggataataca taaaataata ggtaaaccta acgtcagcgc accttttctt
     2101 cgagctgttt tagcatcgaa atatcaccta ataaccgttg atttttacct gtgaaaaaga
     2161 tgatcggact gacatttgca ttatcaatac ttcggcttaa ctgaattccc atcgcctgat
     2221 aatcatcatc gtttgtgcaa tggtataacg ctaaaacaag ctgacattgt tctggagttc
     2281 cgcattctat tgcccagcgg atcaactccg aaaaggtcaa tccgttcggt ttccagtgtt
     2341 ttttatgccg tgacgctaac gccttaaatt tttcacgccc ttgattatat ttttctgccc
     2401 cgatcaccgg atcttcacaa cgaacccctt gaaccggtcg cttatcaaat gacaattccc
     2461 ataaatttaa ttcttcgatg tattcgtaat cttctggcga tgccaaacga aataattgag
     2521 acatagagac accctccgat catgtgtgaa cggagacagt ataaggcttt cgagaaattc
     2581 cgcttcctcg acgtgaaaca agttcacgcc ttgcggcgag cgttgcgaat tgaatttatg
     2641 aggtttacca agctccagat gtaacaaagc cccgtgacag cat
//
