LOCUS       NZ_CP041440             4072 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain YPE12 plasmid pYPE12-Col, complete sequence.
ACCESSION   NZ_CP041440
VERSION     NZ_CP041440.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12233489
            Assembly: GCF_008807155.1
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  JOURNAL   Unpublished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_008807155.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 03:26:26
            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)                     :: 5,017
            CDSs (total)                      :: 4,899
            Genes (coding)                    :: 4,644
            CDSs (with protein)               :: 4,644
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 255
            CDSs (without protein)            :: 255
            Pseudo Genes (ambiguous residues) :: 0 of 255
            Pseudo Genes (frameshifted)       :: 79 of 255
            Pseudo Genes (incomplete)         :: 176 of 255
            Pseudo Genes (internal stop)      :: 39 of 255
            Pseudo Genes (multiple problems)  :: 36 of 255
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041440.1.
            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="YPE12"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pYPE12-Col"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.24 N 119.26 E"
                     /collection_date="2019-06"
                     /collected_by="Xiaoyu Lu"
     gene            join(3398..4072,1..33)
                     /locus_tag="FNP80_RS00765"
                     /old_locus_tag="FNP80_00760"
     CDS             join(3398..4072,1..33)
                     /locus_tag="FNP80_RS00765"
                     /old_locus_tag="FNP80_00760"
                     /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(288..2435)
                     /gene="mobQ"
                     /locus_tag="FNP80_RS00770"
                     /old_locus_tag="FNP80_00765"
     CDS             complement(288..2435)
                     /gene="mobQ"
                     /locus_tag="FNP80_RS00770"
                     /old_locus_tag="FNP80_00765"
                     /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            2614..2868
                     /gene="mobC"
                     /locus_tag="FNP80_RS00775"
                     /old_locus_tag="FNP80_00770"
     CDS             2614..2868
                     /gene="mobC"
                     /locus_tag="FNP80_RS00775"
                     /old_locus_tag="FNP80_00770"
                     /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(2078..2436)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.722"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2437..2613
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3399..4072
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.259"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(292..2522)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaggaagaca aacagatcaa gatgacgatc tagaatcgat tttaaggcac ctaaaacgct
       61 ctctgttgcg ttttttccat gagaggtatg cgatggtact actggtgaga taaaattgct
      121 tcataatcga ttctatggcg ttcaaaaaaa agaaccccca acttagtggg ggcgggaaaa
      181 cgataaagtt ggatttgtgc aatctgtgtg catctgacat tcatccagtt acgatgaatg
      241 tcagagaaca taacacgatg taaaacaaaa caaaatacta tcagcagtta ccgtgaacag
      301 tcgcgatcat ttttcttccc ggagacacgt gttcgtgcat gctcctcgcg ccgccattca
      361 tcccaggtgt gattaaagcc cagtgaacgg aacagatgat ccggctgttt ttctggtgtg
      421 ttgacggcag caaaaagcgg tgtctcgcgg gttttaagat gaaacgccat aagttccggt
      481 gcaggtgaaa tgtggttgtc tgcatcgtga tttacggcaa caccatatcc tgcatatcgt
      541 aaccccttat cggtcagcgc actgatgacc agatgcctgt tatcggcgga ggggacagca
      601 aacgcgggat acagcgaacc attaagccgg acaacaccgc ccagagagtc atccacgccc
      661 atgaccagca aaagctgaag ttgtcggttt tcccggtcga cagaactcat taccggcatc
      721 agcgtcggtg gcagacgtcc ctgcgtaaaa tccaccctcc ttgccaccgg tgatggcatg
      781 gctggctggc ggttttctcc aagacagaaa gactccggcc atgtcttcgg ctggcggaga
      841 ttgcgggtat gttgcggcca tgtctggcaa acctgcgtca gaagttgctc aaaggtcgca
      901 gaggaataaa cacgttgcag tggtggatgt tgaccgattt cgcttcggtc acagatataa
      961 ccactcctgt cacgcattaa atcaacactc tcaaagatcc tggtgcggta tttctccagc
     1021 tcgttccccc agagcgtata ttctccgttc cggttgtgaa gcagaaggta acaggtcatt
     1081 tccccgttac caggcatggg agcctcgcca tatcccgtaa cgactgctct cagcacccct
     1141 gaatccataa cggcattgtc atttttcctg agctgctccg cgcgactacg ttctgtatcc
     1201 tccagctcct tccggcgcaa ttcctcttca cgtttaagca actgggatct gagagctgca
     1261 aggccggatt ccccccactg ctgccactgt ttttcaaatg ccgtctgact cgcgggaatg
     1321 tcctgtttct ccaccttccg gtaatgctgt cgcaattttt ccatttgctg gctcagagac
     1381 tggatttttc cctgctcact acggtattcc ggtgcagccc attgcatcag gggaatacgg
     1441 gaaaaaccgg acgaaaacgg cgatgatttt ttcaggctgg cagcatggct catcgcttcc
     1501 tttcgttcgg tgttcagctc ttcccagcgt ctgcgtgtcg cctgcatatc tgccatcatc
     1561 gacatggcgt tactggtgag tttccatgcc gcgttactgt ccttcggcaa cgcttcgatg
     1621 atgtcacgta gtgtgtacga agttgcgttg tcaggaagcc cgatcttcag aaggtcagcc
     1681 acacggcggg caggctctgt cagcccgctg ttcctgagtt cggtgcggga aatctgtatt
     1741 tccaggttaa gcctgttaat cagacgattc tgttcgccgc gttctgtttc gataccgcgt
     1801 gtttccatcg cacaggcaga ctttccgagg tgaataccag gcgttttctc aagcccctgt
     1861 cgctcgtatg aacgatggtc tatctcttcc tgataaccgg cgttcgccag tgccctgttt
     1921 gcatggtcag cccatgatgc ccgccacgtc tcggcatgtg tccggtcgtt ccagtccctg
     1981 acctttccgc tgaacccagc aggtccgata gccctcgtgg tcagcatgat gtgcgcatgg
     2041 ggatttgttt tatccatgtg atggaacgcc acatcagcaa tcatgccctg actgacaaag
     2101 ttttctctga caaaggcgag aacggtttcc cgggcggcat cctgcggcag ttcgtggggg
     2161 atggcgagtt caatttcccg cgcaagttgt gagttcttcc ggcgttcggc cttctcaacg
     2221 gcattccaga gttcggcacg gttcgtacac caggcagggg cggtggcggg ggtcagaatc
     2281 acagcctcag ccacaccgct tttgcgggtg tagtcgtgag tcagtccggt acgctcatca
     2341 agcatcagtg aaccggaacg ataggcagcg gaagctacgg cgctgtagcc gctgcttctg
     2401 gagataattt tcatgctgag atgataaatc gccatttctg ccgtaatgcc tttttgtagt
     2461 tttctttcag ccccgcaggg cgcacacaat cgaaacggag tggagattgt ataagtgcgc
     2521 acttcgtgat ttgccgtgca ttatgccagc tcagttttta aactaccagt gacgcgctaa
     2581 aatgcgattt ttcatcgcgc acggagttac atcatgagca gaacgctcga acagaagatt
     2641 gctgatgctg aggcgagatt acagcgcctg aaggcgaaga gccggagcct ggacacagcg
     2701 cagaaggttg ttgtgggtgc tgcattgctg gcaaaggtca gaaagccgga ggaggtgcag
     2761 ttgcgtgcct ggttactcca gttcctgaag gcagaggtga cacgacaggc tgatgtgacg
     2821 cgcatactgc cgctgattaa cgagctggag gcgctgccag aacagtgatt gtatcgtccg
     2881 ctcgccgcag cccagcgacc gagcgttagc gagcgagtgg gcgaggaagc ggaagtgaat
     2941 cagtcgccat gttgagcaca tacgcacggt ttttcgacag gtgatatgcg ctgaacccgc
     3001 atgaatactg gatttccaca gggttggagg gggggtattc ggaatctcca atcctgattt
     3061 tttgcaacac attgttttta ttgggttttt attttcagca ctccaagtta tccacaggct
     3121 cgccgttaag tttttagatc ttgtttttaa tacttgtttt taatacttgt tttagggtcg
     3181 aaattcctga ttaaaaacaa tgcgttacac gtgtataggt ggggaaattt aaggtaaagg
     3241 tgatataatt taaggttctt gggtgaggta atttaaggta aaggtgagga gatttaaggt
     3301 aatattcaca gaaaaatggg gggtggaaat ataattgctc accaatgcta aaggtgatag
     3361 gtttttatct cacctcatct ttggcctggt ggttaaaatg acatcaaacc ctctgatagc
     3421 ctataagtcc aatgcgctgg ttgaggccag ttacaagcta actttacaag aacagcgttt
     3481 cttattgctc tgcataagcc gacttaactc cggtactgac gtagcttcac ctgaattgca
     3541 aaagacaatg accattacag ctgcggaata ttttgattca ttccctgata tggggcggaa
     3601 aaatgccgag gttcagctac aggaagcgat cgatcgtttg tgggacaggt cgatcattct
     3661 caaggacgac gagaagcgcg aggagttccg ctggattcag tatcgggcac agtacgcgag
     3721 gggagagggg aaagcacaaa tcactttttc tgacgcggta atgccttatc tgacacagtt
     3781 gaaggggcaa ttcaccagag ttgttattaa aaatatctcc aatttatcaa gaagttacag
     3841 cataagaata tacgagattc tccagcaatt ccgcagtact ggggaacgta ttatcgccct
     3901 cgatgatttt aaatcatcac tgatgcttga tggtaaatat aaagatttca aaacgttaaa
     3961 cagggatcta ataaaaccct gtgttgacga actgaacaaa aaaagcgacc tggctgtaac
     4021 ggttgagacg atcaaaaagg ggcgcacggt tgtagccctg cattttcgct tc
//
