LOCUS       NZ_CP090309             4665 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Escherichia coli strain Z503 plasmid p503-colRNA, complete sequence.
ACCESSION   NZ_CP090309
VERSION     NZ_CP090309.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24295374
            Assembly: GCF_022558405.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4665)
  AUTHORS   Li,Y., Zhang,R. and Wang,S.
  TITLE     A Natural Novel Mutation in the blaNDM-5 Promoter Reducing
            Carbapenems Resistance in a Clinical Escherichia coli Strain
  JOURNAL   Microbiol Spectr 10 (1), e0118321 (2022)
   PUBMED   35138141
REFERENCE   2  (bases 1 to 4665)
  AUTHORS   Li,Y., Zhang,R. and Wang,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-DEC-2021) College of Veterinary Medicine, China
            Agricultural University, 2nd West Yuanmingyuan Rd, Beijing 100193,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SPAdes v. 3.9.0; Unicycle v. NOV-2018
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina Hiseq2500; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022558405.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:36:01
            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)                     :: 4,561
            CDSs (total)                      :: 4,445
            Genes (coding)                    :: 4,199
            CDSs (with protein)               :: 4,199
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 246
            CDSs (without protein)            :: 246
            Pseudo Genes (ambiguous residues) :: 0 of 246
            Pseudo Genes (frameshifted)       :: 66 of 246
            Pseudo Genes (incomplete)         :: 172 of 246
            Pseudo Genes (internal stop)      :: 40 of 246
            Pseudo Genes (multiple problems)  :: 32 of 246
            Pseudo Genes (short protein)      :: 4 of 246
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP090309.1.
            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..4665
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Z503"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p503-colRNA"
                     /geo_loc_name="China: Zhejiang"
                     /collection_date="2018-08-14"
     gene            join(4516..4665,1..195)
                     /locus_tag="LXF06_RS22620"
     CDS             join(4516..4665,1..195)
                     /locus_tag="LXF06_RS22620"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_032967811.1"
                     /translation="MSEKRNKMLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPAR
                     SGKLPSISPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHA
                     VLEKGTDDDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            404..>838
                     /locus_tag="LXF06_RS22625"
                     /pseudo=""
     CDS             404..>838
                     /locus_tag="LXF06_RS22625"
                     /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            873..1358
                     /locus_tag="LXF06_RS22630"
     CDS             873..1358
                     /locus_tag="LXF06_RS22630"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_012565228.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1362..1577
                     /locus_tag="LXF06_RS22635"
     CDS             1362..1577
                     /locus_tag="LXF06_RS22635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_015589619.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1923..3479
                     /locus_tag="LXF06_RS22640"
     CDS             1923..3479
                     /locus_tag="LXF06_RS22640"
                     /EC_number="2.7.7.65"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015589620.1"
                     /GO_function="GO:0052621 - diguanylate cyclase activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WP_226426401.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGARKIKSTNDIDSLKDEADRLRLQSGMFNSVFV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAIEEKKPFISSPFKSVTGNLIILLSHPIYD
                     KNGNYIGHVGGSIYLKKHSLFSDVLSRHFFKSDTEISIVSDDGTVIFNNDNSAVGRPMV
                     MSDDLKSKLTESDRGEGAFFSSGNRYLLGYAHMKNPAWNVLVYSHADSATTILITYAKS
                     VLVLLIVIIITFSLLSYFIASRISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTHVKVMMERVDSLNEMALKDPLTGVNNRLGFLSKIQNHKRDSGYSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     Typing          4252..4424
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(3775..4327)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.46"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          186..1681
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.982"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4538..4665
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.349"
                     /coverage="99.0"
                     /evalue="5.550000000000001e-21"
ORIGIN
        1 tcaatctcgc cggcgctgct gcgccagctt gccggcatgg gcaataacct gaaccagata
       61 gcccgccgtg ttaacgccgg cggcggtacc ggccatgaca gggtgcagat tgttgcggcg
      121 ctgatggcca tcgatgccgg acttgagcgg ctgcggcacg ccgttcttga gaaaggaacg
      181 gacgatgatc gttaaatttc atccacgcgg tcgcggcggt ggcgccgggc cggtggacta
      241 tctgctgggt aaagaccggc agcgtgaagg cgccaccgtc ctgcagggga agccggaaga
      301 agtccgggag ctgattgacg cgtcgcctta cgttaagaaa tacacctccg gggtactgtc
      361 gtttgcggaa gcggatttac cttccggcca gcgggaaaag ctgatggcaa gctttgagcg
      421 ggttctgatg cccggacttg ataaagacca gtacagcatc ctgtgggtgg agcatcgtga
      481 caaggggcgg cttgagctga attttctgat cccgaacacg gagctgctga ccggcagacg
      541 gctccagccg tattacgatc gcgccgaccg tccacgcatc gatgcctggc agaccatcgt
      601 gaacggcaga ctggggctgc acgacccgaa cgcaccggag aaccggcggg cactggtcac
      661 accgtctgca ctgcctaaag cgaagcagga ggctgcagaa gcgattacat gcggtctgct
      721 tgctcttgcc tcatccgggg agctgaaaac ccgtcaggat gtcactgagg cgctggaaag
      781 cgcaggtttt gaggtggtcc gcaccacaaa aagcagtatc agcattgccg acccggacgg
      841 ggggcgaaac atccgactga agggagccat ttatgaacag tcttttaacg ctggcgaagg
      901 acttagagca gaaatcgaaa gcgcagcagc agaataccgg cgagatgctg aaagccgcat
      961 tcagcgagca cgagaaatct gtaaaagcgg aactgaacga aagcgcgaag agaatcagcg
     1021 ccgccatcct cgaccacgac cggaaactgt cctcagccat gagccagcgc acgaaaggca
     1081 tggtgcgcat ggtcagccag acgtggctga ccatcgtcct ggtctccgcg ctgctgatcg
     1141 cctcgagcgc gggcattctg tggtggcagg ggcagcagat actcgacaac tacacgacca
     1201 tccgggagca gaagagcacg caggccatgc tgtcagagag gaacagcggc gtgcagctct
     1261 cgacctgcgg cgagcagaga cgccgctgcg tgaaggtgaa cccggaagcg ggacggttcg
     1321 gagaggattc gagctggatg atactggcgg ggaaatagca catgacggag ctggaaaaac
     1381 agttgctgag cgcattagag cagctacagc aggactactc gaaaaggctg gacgagtggg
     1441 agagcgcctt cgcggaatgg cggacgatgt ctggtcttat gcaacgggag aacgcagcgc
     1501 tgagcgagcg cgtcacgggc ttgagcaggc aggtgcagag tttgagcgag cagctgcgcc
     1561 ggttgtcgag cgactgaatg ccgtcgagct gcaccgggag caggagcgcg tggtgcagca
     1621 tcagaaagcg ctggagctgg agcgatctca gcgacagcgg acgtataaca gcccttcact
     1681 gtgataacct gataaaacgg ggctttcggc ggacatctgc gctgaaagcc ggagccattc
     1741 acccgactgc atagccatgc agccgggtga aatttatctg gcgcagaatg cgcggtttag
     1801 cggagagttt gctgccggtt ttaccgggct gacgccgcat ttgttccgaa cccgtccggg
     1861 gcggtgctga taagggatgt tatggtaaat gcggcatttt ttattatatg gagtgtattt
     1921 ttatgagaat taaaaagcct caccttcgtc cgatagtcat aaccttgtcc gttggtggga
     1981 ttttgttaac ttctattttt ctgattgccg ttattatggt ttttcagcgc gaaaatatag
     2041 aaaaagattt gctttatgct aattcatcgt acgctatgaa aatgtcagat gtaatgagtg
     2101 gttatattga aatggctcaa ggtgaattag catatggagc aagaaaaata aaatcaacta
     2161 atgatattga ctcacttaaa gatgaggcgg ataggttaag attgcagtct ggtatgttta
     2221 attcagtttt tgttgttagt aatgatgctg ttgttctggc gacttcgcca gaatctcttg
     2281 atttagttgg tacccgcttg aattcaagtg ccagcaaatt ggcgattgag gaaaagaaac
     2341 cattcatatc ttcaccgttc aaatcagtta ctgggaattt gattattttg ttgtcacatc
     2401 ctatttatga taagaatggc aattacatag ggcatgtcgg tgggtctata tatctaaaaa
     2461 aacatagttt atttagcgat gttttgagca ggcatttttt caagagcgac actgaaatta
     2521 gcattgttag tgatgatgga actgtgatct ttaataacga taacagtgct gttggtcggc
     2581 ccatggttat gtctgatgat ttgaaatcaa agttaacgga gtctgataga ggtgaggggg
     2641 catttttttc ttcggggaat agatatcttc tgggttatgc tcatatgaaa aatcctgctt
     2701 ggaatgtgtt ggtttatagc catgctgaca gcgcgactac tattcttatt acttatgcta
     2761 aaagtgtact tgttctgcta attgtaataa ttattacatt ttcacttctt tcatatttca
     2821 ttgcctcccg tatttcactt cctttagaaa agcttgctat atctaccaat gctaaagata
     2881 taggggcttc gttagtttat attaaagcta tcaatgcttg gtatgccgaa gctgatcgac
     2941 ttaaaaaggc actttttacg catgttaagg taatgatgga aagggttgat tctttaaatg
     3001 agatggcgct taaagatccc cttaccggcg tgaacaatag attggggttt ttaagtaaaa
     3061 tacagaatca taagcgggat tcagggtatt cagttattgt aattgatgtt gattttttta
     3121 aagagataaa tgacagtttc gggcatgggg tcggagatga ggtgcttgtt tctttggctc
     3181 atattattaa ttcctgttgc cgtagtgaag atgttgtttg tcggtttggt ggcgaagagt
     3241 ttgttgtttt cctgccgaat acatctgtgg taacagctaa gtgtgttgcg gagcgtatta
     3301 ggagtgttat tgaaagtact gtcttcccta ataacttgcg ggtcaccata tctgctggtg
     3361 tggcaacaca agatgatcct cttggtagga tcgatttttt gctgaaaaat gctgacgatg
     3421 ctctttatca agccaaaagg gaggggcgta ataaagtgat tgtatatagc gctatttgag
     3481 ttttttgatg atgctttacg cgctagtgtg tcgttttttt tgtggcgaag agtgggcaag
     3541 aagcggatcc tcttgttatc ccttcgatgt cgtcgtaatc tcataccctg taaacaaaaa
     3601 aaccaccgct accaacggtg gttcgtttgc cggaattcag agctaccaac tctttcttcc
     3661 gaaggtaact ggctttcacg gagcgcaggt accaaaactg tccttccagt gtagccgcag
     3721 tcaggccacc acttcaagaa ctctgtagaa cactctacta ctccgctccg tgaatcctct
     3781 tactaatggc taccgccact ggcgattttt cgtgtctgtt ccgggttgga ctcaagatga
     3841 tagttaccgg gacaacgtgg tagtcgggct gaacgggggg ttcgtgcata cagtccagct
     3901 tggagcgaac tgccttcccg gaaccgagtg tcaggcgtgg aatgagataa acgcggccat
     3961 aacagcggat tgacatcggt aaaccgaaag gcaggaacag gagagcgcac gagggagcca
     4021 ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacca ctgatttgag
     4081 cgtcagattt cgtgatgctt gtcagggggg cggagcctat ggaaaaacgg cttcgccgtg
     4141 gccttatcgc ttccctgtta agcttcttcc tggcatctcc caggaaattt ccgccccgcc
     4201 tgtaagccgg taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg
     4261 aagcggaata tatcctgtat cacatattct gctgacgctc cgctgctgca tttttctcct
     4321 gccacatgaa gcacttcact gacactcgca tccgtgccaa catagtaagc cagtatacac
     4381 tccgctagcg ctacgtgact ggttcagggc tgcgccccga aacccgccaa aagcctgacg
     4441 cgcctgcggc ttgtccaacc ccgcgccgac cgggaaaggc tttcccgccc gtcccggcgt
     4501 tatcaggagg ccggtttgtc agagaaacgg aacaagatgc tcaccatgtg ggtgacggag
     4561 gacgagcacc ggcggctgct tgagcgctgc gacggcaggc agctggcagc gtggatgcgg
     4621 cagacctgcc tggacgaaaa gccggcacgt tccggaaagc ttccc
//
