LOCUS       NZ_CP041450             4072 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain YPE3 plasmid pYPE3-Col, complete sequence.
ACCESSION   NZ_CP041450
VERSION     NZ_CP041450.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12233487
            Assembly: GCF_008807295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Li,R., Lu,X., Liu,Z., Liu,Y., Xiao,X. and Wang,Z.
  TITLE     Application of Nanopore Sequencing for Rapid Characterization of
            tet(X4)-positive E. coli strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Li,R., Lu,X., Liu,Z., Liu,Y., Xiao,X. and Wang,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2019) College of Veterinary Medicine (Institute of
            Comparative Medicine), Yangzhou University, Wenhui Road, Yangzhou,
            Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80X
            Sequencing Technology :: Oxford Nanopore MinION, Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_008807295.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 03:11:21
            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)                     :: 4,764
            CDSs (total)                      :: 4,643
            Genes (coding)                    :: 4,437
            CDSs (with protein)               :: 4,437
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 63 of 206
            Pseudo Genes (incomplete)         :: 143 of 206
            Pseudo Genes (internal stop)      :: 38 of 206
            Pseudo Genes (multiple problems)  :: 32 of 206
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041450.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YPE3"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pYPE3-Col"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.24 N 119.26 E"
                     /collection_date="2019-06"
                     /collected_by="Xiaoyu Lu"
     gene            join(3624..4072,1..1699)
                     /gene="mobQ"
                     /locus_tag="FNP78_RS00005"
                     /old_locus_tag="FNP78_00005"
     CDS             join(3624..4072,1..1699)
                     /gene="mobQ"
                     /locus_tag="FNP78_RS00005"
                     /old_locus_tag="FNP78_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_151140345.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLKIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGENRQPAMPSPVARRVDFTQGRLPPTLMPVM
                     SSVDRENRQLQLLLVMGVDDSLGGVVRLNGSLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADNHISPAPELMAFHLKTRETPLFAAVNTPEKQPDHLFRSLGFNHTWDEW
                     RREEHARTRVSGKKNDRDCSR"
                     /name="mobQ"
     gene            complement(1954..2661)
                     /locus_tag="FNP78_RS00010"
                     /old_locus_tag="FNP78_00010"
     CDS             complement(1954..2661)
                     /locus_tag="FNP78_RS00010"
                     /old_locus_tag="FNP78_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3191..3445)
                     /gene="mobC"
                     /locus_tag="FNP78_RS00020"
                     /old_locus_tag="FNP78_00020"
     CDS             complement(3191..3445)
                     /gene="mobC"
                     /locus_tag="FNP78_RS00020"
                     /old_locus_tag="FNP78_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3447..3623)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3624..3982
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.722"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1955..2661)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.294"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1696
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.673"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaaggtcagg gactggaacg accggacaca tgccgagacg tggcgggcat catgggctga
       61 ccatgcaaac agggcactgg cgaacgccgg ttatcaggaa gagatagacc atcgttcata
      121 cgagcgacag gggcttgaga aaacgcctgg tattcacctc ggaaagtctg cctgtgcgat
      181 ggaaacacgc ggtatcgaaa cagaacgcgg cgaacagaat cgtctgatta acaggcttaa
      241 cctggaaata cagatttccc gcaccgaact caggaacagc gggctgacag agcctgcccg
      301 ccgtgtggct gaccttctga agatcgggct tcctgacaac gcaacttcgt acacactacg
      361 tgacatcatc gaagcgttgc cgaaggacag taacgcggca tggaaactca ccagtaacgc
      421 catgtcgatg atggcagata tgcaggcgac acgcagacgc tgggaagagc tgaacaccga
      481 acgaaaggaa gcgatgagcc atgctgccag cctgaaaaaa tcatcgccgt tttcgtccgg
      541 tttttcccgt attcccctga tgcaatgggc tgcaccggaa taccgtagtg agcagggaaa
      601 aatccagtct ctgagccagc aaatggaaaa attgcgacag cattaccgga aggtggagaa
      661 acaggacatt cccgcgagtc agacggcatt tgaaaaacag tggcagcagt ggggggaatc
      721 cggccttgca gctctcagat cccagttgct taaacgtgaa gaggaattgc gccggaagga
      781 gctggaggat acagaacgta gtcgcgcgga gcagctcagg aaaaatgaca atgccgttat
      841 ggattcaggg gtgctgagag cagtcgttac gggatatggc gaggctccca tgcctggtaa
      901 cggggaaatg acctgttacc ttctgcttca caaccggaac ggagaatata cgctctgggg
      961 gaacgagctg gagaaatacc gcaccaggat ctttgagagt gttgatttaa tgcgtgacag
     1021 gagtggttat atctgtgacc gaagcgaaat cggtcaacat ccaccactgc aacgtgttta
     1081 ttcctctgcg acctttgagc aacttctgac gcaggtttgc cagacatggc cgcaacatac
     1141 ccgcaatctc cgccagccga agacatggcc ggagtctttc tgtcttggag aaaaccgcca
     1201 gccagccatg ccatcaccgg tggcaaggag ggtggatttt acgcagggac gtctgccacc
     1261 gacgctgatg ccggtaatga gttctgtcga ccgggaaaac cgacaacttc agcttttgct
     1321 ggtcatgggc gtggatgact ctctgggcgg tgttgtccgg cttaatggtt cgctgtatcc
     1381 cgcgtttgct gtcccctccg ccgataacag gcatctggtc atcagtgcgc tgaccgataa
     1441 ggggttacga tatgcaggat atggtgttgc cgtaaatcac gatgcagaca accacatttc
     1501 acctgcaccg gaacttatgg cgtttcatct taaaacccgc gagacaccgc tttttgctgc
     1561 cgtcaacaca ccagaaaaac agccggatca tctgttccgt tcactgggct ttaatcacac
     1621 ctgggatgaa tggcggcgcg aggagcatgc acgaacacgt gtctccggga agaaaaatga
     1681 tcgcgactgt tcacggtaac tgctgatagt attttgtttt gttttacatc gtgttatgtt
     1741 ctctgacatt catcgtaact ggatgaatgt cagatgcaca cagattgcac aaatccaact
     1801 ttatcgtttt cccgccccca ctaagttggg ggttcttttt tttgaacgcc atagaatcga
     1861 ttatgaagca attttatctc accagtagta ccatcgcata cctctcatgg aaaaaacgca
     1921 acagagagcg ttttaggtgc cttaaaatcg attctagatc gtcatcttga tctgtttgtc
     1981 ttccttgaag cgaaaatgca gggctacaac cgtgcgcccc tttttgatcg tctcaaccgt
     2041 tacagccagg tcgctttttt tgttcagttc gtcaacacag ggttttatta gatccctgtt
     2101 taacgttttg aaatctttat atttaccatc aagcatcagt gatgatttaa aatcatcgag
     2161 ggcgataata cgttccccag tactgcggaa ttgctggaga atctcgtata ttcttatgct
     2221 gtaacttctt gataaattgg agatattttt aataacaact ctggtgaatt gccccttcaa
     2281 ctgtgtcaga taaggcatta ccgcgtcaga aaaagtgatt tgtgctttcc cctctcccct
     2341 cgcgtactgt gcccgatact gaatccagcg gaactcctcg cgcttctcgt cgtccttgag
     2401 aatgatcgac ctgtcccaca aacgatcgat cgcttcctgt agctgaacct cggcattttt
     2461 ccgccccata tcagggaatg aatcaaaata ttccgcagct gtaatggtca ttgtcttttg
     2521 caattcaggt gaagctacgt cagtaccgga gttaagtcgg cttatgcaga gcaataagaa
     2581 acgctgttct tgtaaagtta gcttgtaact ggcctcaacc agcgcattgg acttataggc
     2641 tatcagaggg tttgatgtca ttttaaccac caggccaaag atgaggtgag ataaaaacct
     2701 atcaccttta gcattggtga gcaattatat ttccaccccc catttttctg tgaatattac
     2761 cttaaatctc ctcaccttta ccttaaatta cctcacccaa gaaccttaaa ttatatcacc
     2821 tttaccttaa atttccccac ctatacacgt gtaacgcatt gtttttaatc aggaatttcg
     2881 accctaaaac aagtattaaa aacaagtatt aaaaacaaga tctaaaaact taacggcgag
     2941 cctgtggata acttggagtg ctgaaaataa aaacccaata aaaacaatgt gttgcaaaaa
     3001 atcaggattg gagattccga ataccccccc tccaaccctg tggaaatcca gtattcatgc
     3061 gggttcagcg catatcacct gtcgaaaaac cgtgcgtatg tgctcaacat ggcgactgat
     3121 tcacttccgc ttcctcgccc actcgctcgc taacgctcgg tcgctgggct gcggcgagcg
     3181 gacgatacaa tcactgttct ggcagcgcct ccagctcgtt aatcagcggc agtatgcgcg
     3241 tcacatcagc ctgtcgtgtc acctctgcct tcaggaactg gagtaaccag gcacgcaact
     3301 gcacctcctc cggctttctg acctttgcca gcaatgcagc acccacaaca accttctgcg
     3361 ctgtgtccag gctccggctc ttcgccttca ggcgctgtaa tctcgcctca gcatcagcaa
     3421 tcttctgttc gagcgttctg ctcatgatgt aactccgtgc gcgatgaaaa atcgcatttt
     3481 agcgcgtcac tggtagttta aaaactgagc tggcataatg cacggcaaat cacgaagtgc
     3541 gcacttatac aatctccact ccgtttcgat tgtgtgcgcc ctgcggggct gaaagaaaac
     3601 tacaaaaagg cattacggca gaaatggcga tttatcatct cagcatgaaa attatctcca
     3661 gaagcagcgg ctacagcgcc gtagcttccg ctgcctatcg ttccggttca ctgatgcttg
     3721 atgagcgtac cggactgact cacgactaca cccgcaaaag cggtgtggct gaggctgtga
     3781 ttctgacccc cgccaccgcc cctgcctggt gtacgaaccg tgccgaactc tggaatgccg
     3841 ttgagaaggc cgaacgccgg aagaactcac aacttgcgcg ggaaattgaa ctcgccatcc
     3901 cccacgaact gccgcaggat gccgcccggg aaaccgttct cgcctttgtc agagaaaact
     3961 ttgtcagtca gggcatgatt gctgatgtgg cgttccatca catggataaa acaaatcccc
     4021 atgcgcacat catgctgacc acgagggcta tcggacctgc tgggttcagc gg
//
