LOCUS       NZ_CP139129             4664 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Escherichia coli strain YZ22PE244 plasmid pYUYZPE244-4, complete
            sequence.
ACCESSION   NZ_CP139129
VERSION     NZ_CP139129.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN38245694
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  AUTHORS   Wang,J.
  TITLE     tet(X4)-positive Escherichia coli strains in Yangzhou
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4664)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-NOV-2023) Key Laboratory of Prevention and Control of
            Biological Hazard Factors (Animal Origin) for Agrifood Safety and
            Quality, Ministry of Agriculture of China, Yangzhou University,
            No.48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 10:55:24
            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)                     :: 5
            CDSs (total)                      :: 5
            Genes (coding)                    :: 4
            CDSs (with protein)               :: 4
            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
            CP139129.1.
            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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YZ22PE244"
                     /isolation_source="Pig farm"
                     /host="pig"
                     /db_xref="taxon:562"
                     /plasmid="pYUYZPE244-4"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.27 N 119.29 E"
                     /collection_date="2022-06-02"
                     /collected_by="Jiang Yue"
     gene            join(4602..4664,1..153)
                     /locus_tag="SIY77_RS00005"
     CDS             join(4602..4664,1..153)
                     /locus_tag="SIY77_RS00005"
                     /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            484..2055
                     /locus_tag="SIY77_RS00010"
     CDS             484..2055
                     /locus_tag="SIY77_RS00010"
                     /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_094304142.1"
                     /translation="MECIFMRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIE
                     KDLLYANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKLTNDIDSLKDEADRLRLQSGMF
                     NSVLVVSNDAVVLATSPESLDLVGTRLNSSASKLAIEEKKPFISSPLKSVTGNLIILLS
                     HPIYDKGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAV
                     DRPMVMSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTTWNVLVYSRADSVTTILI
                     AYAKSVLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYA
                     EADRLKKALFTYIKVMMERVDYLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGYSVIVI
                     DVDFFKEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAK
                     CVAERIRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKV
                     IVYSAI"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            3112..3435
                     /locus_tag="SIY77_RS00015"
     CDS             3112..3435
                     /locus_tag="SIY77_RS00015"
                     /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_015059937.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3644..>4078
                     /locus_tag="SIY77_RS00020"
                     /pseudo=""
     CDS             3644..>4078
                     /locus_tag="SIY77_RS00020"
                     /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            4113..4598
                     /locus_tag="SIY77_RS00025"
     CDS             4113..4598
                     /locus_tag="SIY77_RS00025"
                     /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"
     Typing          2827..2999
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(2351..2902)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          3113..3429
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
     Typing          3426..4663
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.768"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aggctggacg agtgggagag cgccttcgcg gaatggcgga cgatgtctgg tcttatgcaa
       61 cgggagaacg cagcgctgag cgagcgcgtc acgggcttga gcaggcaggt gcagagtttg
      121 agcgagcagc tgcgccggtt gtcgagcgac tgaatgccgt cgagctgcac cgggagcagg
      181 agcgcgtggt gcagcatcag aaagcgctgg agctggagcg atctcagcga cagcggacgt
      241 ataacagccc ttcactgtga taacctgata aaacggggct ttcggcggac atctgcgctg
      301 aaagccggag ccattcaccc gactgcatag ccatgcagcc gggtgaaatt tatctggcgc
      361 agaatgcgcg gtttagcgga gagtttgctg ccggttttac cgggctgacg ccgcatttgt
      421 tccgaacccg tccggggcgg tgctgataag ggatgttatg gtaaatgcgg cattttttat
      481 tatatggagt gtatttttat gagaattaaa aagcctcacc ttcgtccgat agtcataacc
      541 ttgtccgttg gtgggatttt gttaacttct atttttctga ttgccgttat tatggttttt
      601 cagcgcgaaa atatagaaaa agatttgctt tatgctaatt catcgtacgc tatgaaaatg
      661 tcagatgtaa tgagtggtta tattgaaatg gctcaaggtg aattagcata tggagcaaaa
      721 aaaataaaat taactaatga tattgactca cttaaagatg aggcggatag gttaagattg
      781 cagtctggta tgtttaattc agttcttgtt gttagtaatg atgctgttgt tctggcgact
      841 tcgccagaat ctcttgattt agttggtacc cgcttgaatt caagtgccag caaattggcg
      901 attgaggaaa agaaaccatt catatcttca ccgttaaaat cagttactgg gaatttgatt
      961 attttgttgt cacatcctat ttatgataag ggtggcaatt acatagggta tgtcggtggg
     1021 tctatatatc taaaaaaaca tagtttattt ggcgatgttt tgagcaggca ttttttcaag
     1081 aacaacactg aaattagcat tgttagtgat gatgggaatg tgatctttaa taacgataaa
     1141 agtgctgttg atcggcctat ggttatgtct gatgatttga aatcaaagtt aactgcgtct
     1201 gatagaggtg agggggcatt tttttcttcg gggcatagat atcttcttgg ttatgctagt
     1261 atgaaaaata ctacttggaa tgtgttggtt tatagtcgtg ctgacagtgt gactactatt
     1321 cttattgctt atgctaaaag tgtacttgtt ctgctaatta taataattat tgtgttttca
     1381 cttatttcat atttcattgc ctccagtatt tcacttcctt tagaaaagct tgctatatct
     1441 accaatgcta aagatatcgg agcttcgcta gtttatatta aagctatcaa tgcttggtat
     1501 gccgaagctg ataggcttaa aaaggcgctt tttacgtata ttaaggtaat gatggaaaga
     1561 gttgattatc taaatgaggt ggcgcttaaa gatcccctta ccggcgtgaa caatagattg
     1621 gggtttttaa gtaaaataca gaatcataag cgggattcag ggtattcagt tattgtaatt
     1681 gatgttgatt tttttaaaga gataaatgac agtttcgggc atggggtcgg agatgaggtg
     1741 cttgtttctt tggctcatat tattaattcc tgttgccgta gtgaagatgt tgtttgtcgg
     1801 tttggtggcg aagagtttgt tgttttcctg ccgaatacat ctgtggtaac agctaagtgt
     1861 gttgcggagc gtattaggag tgttattgaa agtactgtct tccctaataa cttgcgggtc
     1921 accatatctg ctggtgtggc aacacaagat gatcctcttg gtaggatcga ttttttgctg
     1981 aaaaatgctg acgatgctct ttatcaagcc aaaagggagg ggcgtaataa agtgattgta
     2041 tatagcgcta tttgagtttt ttgatgatgc tttacgcgct agtgtgtcgt tttttttgtg
     2101 gcgaagagtg ggcaagaagc ggatcctctt gttatccctt cgatgtcgtc gtaatctcat
     2161 accctgtaaa caaaaaaacc accgctacca acggtggttc gtttgccgga attcagagct
     2221 accaactctt tcttccgaag gtaactggct ttcacggagc gcaggtacca aaactgtcct
     2281 tccagtgtag ccgcagtcag gccaccactt caagaactct gtagaacact ctactactcc
     2341 gctccgtgaa tcctcttact aatggctacc gccactggcg atttttcgtg tctgttccgg
     2401 gttggactca agatgatagt taccgggaca acgtggtagt cgggctgaac ggggggttcg
     2461 tgcatacagt ccagcttgga gcgaactgcc ttcccggaac cgagtgtcag gcgtggaatg
     2521 agataaacgc ggccataaca gcggattgac atcggtaaac cgaaaggcag gaacaggaga
     2581 gcgcacgagg gagccaccag ggggaaacgc ctggtatctt taagtcctgt cgggtttcgc
     2641 caccactgat ttgagcgtca gatttcgtga tgcttgtcag gggggcggag cctatggaaa
     2701 aacggcttcg ccgtggcctt atcgcttccc tgttaagctt cttcctggca tctcccagga
     2761 aatttccgcc ccgcctgtaa gtcggtaccg ctcgccgcag ccgaacgacc gagcgcagcg
     2821 agtcagtgag cgaggaagcg gaatatatcc tgtatcacat attctgctga cgctccgctg
     2881 ctgcattttt ctcctgccac atgaagcact tcactgacac tcgcatccgt gccaacatag
     2941 taagccagta tacactccgc tagcgctacg tgactggttc agggctgcgc cccgaaaccc
     3001 gccaaaagcc tgacgcgcct gcggcttgtc caaccccgcg ccgaccggga aagcctttcc
     3061 cgcccgtccc ggcgttatca ggaggccggt ttgtcagaga aacggaacaa gatgctcacc
     3121 atgtgggtga cggagggcga gcaccggcgg ctgcttgagc gctgtgacgg caggcagctg
     3181 gcggcgtgga tgcggcagac ctgcctggac gaaaagccgg cacgttccgg aaagcttccc
     3241 tcaatctcgc cggcgctgct gcgccagctt gccggcatgg gcaataacct gaaccagata
     3301 gcccgccgtg ttaacgccgg cggcggtacc ggccatgaca gggtgcagat tgttgcggcg
     3361 ctgatggcca tcgatgccgg acttgagcgg ctgcggcacg ccgttcttga gaaaggaacg
     3421 gacgatgatc gttaaatttc atccacgcgg tcgcggcggt ggcgccgggc cggtggacta
     3481 tctgctgggt aaagaccggc agcgtgaagg cgccaccgtc cagcagggga agccggaaga
     3541 agtccgggag ctgattgacg cgtcgcctta cgttaagaaa tacacctccg gggtactgtc
     3601 gtttgcggaa gcggatttac cttccggcca gcgggaaaag ctgatggcaa gctttgagcg
     3661 ggttctgatg cccggacttg ataaagacca gtacagcatc ctgtgggtgg agcatagtga
     3721 caaggggcgg cttgagctga attttctgat cccgaacacg gagctgctga ccggcagacg
     3781 gctccagccg tattacgatc gcgccgaccg tccacgcatc gatgcctggc agaccatcgt
     3841 gaacggcaga ctggggctgc acgacccgaa cgcaccggag aaccggcggg cactggtcac
     3901 accgtctgca ctgcctaaag cgaagcagga ggctgcagaa gcgattacac gcggtctgct
     3961 tgctcttgcc tcatccgggg agctgaaaac ccgtcaggat gtcactgagg cgctggaaag
     4021 cgcaggtttt gaggtggtcc gcaccacaaa aagcagtatc agcattgccg acccggacgg
     4081 ggggcgaaac atccgactga agggagccat ttatgaacag tcttttaacg ctggcgaagg
     4141 acttagagca gaaatcgaaa gcgcagcagc agaataccgg cgagatgctg aaagccgcat
     4201 tcagcgagca cgagaaatct gtaaaagcgg aactgaacga aagcgcgaag agaatcagcg
     4261 ccgccatcct cgaccacgac cggaaactgt cctcagccat gagccagcgc acgaaaggca
     4321 tggtgcgcat ggtcagccag acgtggctga ccatcgtcct ggtctccgcg ctgctgatcg
     4381 cctcgagcgc gggcattctg tggtggcagg ggcagcagat actcgacaac tacacgacca
     4441 tccgggagca gaagagcacg caggccatgc tgtcagagag gaacagcggc gtgcagctct
     4501 cgacctgcgg cgagcagaga cgccgctgcg tgaaggtgaa cccggaagcg ggacggttcg
     4561 gagaggattc gagctggatg atactggcgg ggaaatagca catgacggag ctggaaaaac
     4621 agttgctgag cgcattagag cagctacagc aggactactc gaaa
//
