LOCUS       NZ_CP125354             5686 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Escherichia fergusonii strain XJ19MCE1 plasmid pYUXJMC1-4, complete
            sequence.
ACCESSION   NZ_CP125354
VERSION     NZ_CP125354.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34575413
            Assembly: GCF_030035445.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5686)
  AUTHORS   Wang,J.
  TITLE     Complete sequence of mcr-1-positiveEscherichia fergusonii XJ19MCE1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5686)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-MAY-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 :: non-hybrid Hierarchical Genome Assembly Process
            v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: PacBio single-molecule real-time sequencing
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030035445.1-RS_2024_05_18
            Annotation Date                   :: 05/18/2024 05:12:11
            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)                     :: 4,999
            CDSs (total)                      :: 4,879
            Genes (coding)                    :: 4,696
            CDSs (with protein)               :: 4,696
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 66 of 183
            Pseudo Genes (incomplete)         :: 90 of 183
            Pseudo Genes (internal stop)      :: 42 of 183
            Pseudo Genes (multiple problems)  :: 13 of 183
            Pseudo Genes (short protein)      :: 1 of 183
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP125354.1.
            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..5686
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="XJ19MCE1"
                     /isolation_source="chicken meat"
                     /db_xref="taxon:564"
                     /plasmid="pYUXJMC1-4"
                     /geo_loc_name="China: Xinjiang"
                     /lat_lon="42.45 N 86.37 E"
                     /collection_date="2019"
                     /collected_by="Yan Wang"
     gene            17..208
                     /locus_tag="QKW25_RS24610"
     CDS             17..208
                     /locus_tag="QKW25_RS24610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165974.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(360..674)
                     /locus_tag="QKW25_RS24615"
     CDS             complement(360..674)
                     /locus_tag="QKW25_RS24615"
                     /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_224157910.1"
                     /translation="MSVDFCDARQGGGAYGKNASGAAFFALCLFAHMFFPALSPDSVDN
                     RIAVFEQADSARRSRTTERSESVSEEAEKRLDVHFLLTHLCGISHPAWCTFHTMRPDAE
                     "
                     /name="hypothetical protein"
     gene            complement(1221..2288)
                     /locus_tag="QKW25_RS24620"
     CDS             complement(1221..2288)
                     /locus_tag="QKW25_RS24620"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="WP_001009472.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPVLE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKDIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            2365..3495
                     /locus_tag="QKW25_RS24625"
     CDS             2365..3495
                     /locus_tag="QKW25_RS24625"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_000216732.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(3879..4112)
                     /locus_tag="QKW25_RS24630"
     CDS             complement(3879..4112)
                     /locus_tag="QKW25_RS24630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4119..4637)
                     /locus_tag="QKW25_RS24635"
     CDS             complement(4119..4637)
                     /locus_tag="QKW25_RS24635"
                     /function="essential for mobilization of the plasmid"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_031942530.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4675..5373)
                     /locus_tag="QKW25_RS25005"
                     /pseudo=""
     CDS             complement(<4675..5373)
                     /locus_tag="QKW25_RS25005"
                     /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            complement(5315..5638)
                     /locus_tag="QKW25_RS24645"
     CDS             complement(5315..5638)
                     /locus_tag="QKW25_RS24645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(294..373)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.67e-34"
     Typing          405..947
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.698"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3776..5325)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.374"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttacacggag gcatcagtga ctaaacagga aaaaaccgcc cttaacatgg cccgtttcat
       61 cagaggccag acattaacgc tgctggagaa acttaacgaa ctggacgcag atgaacaggc
      121 agatatctgt gaatcgcttc acgaccacgc cgatgagctt taccgcagct gcctcgcacg
      181 tttcggggat gacggtgaaa acctctgaca catgcagctc ccggaaacgg tcacagcttg
      241 tctgtgagcg gatgccggga gccgacaagc ccgtcaggac gcgtcagcgg gttttagcgg
      301 gtgtcggggc gcagccctga cccagtcacg tagcgatagc ggagtgtata ctggcttact
      361 tattcggcat cagggcgcat tgtatgaaaa gtgcaccatg ccgggtgtga aatgccgcac
      421 agatgcgtaa ggagaaaatg cacgtccagg cgcttttccg cttcctcgct cactgactcg
      481 ctgcgctcgg tcgttcgact gcggcgagcg gagtctgctt gctcaaaaac ggcaatacgg
      541 ttatccacag aatcagggga taaggccgga aagaacatgt gagcaaaaag acaaagggca
      601 aaaaaagccg cgccgctggc gttttttcca taggctccgc ccccctgacg agcatcacaa
      661 aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt
      721 tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta ccggatacct
      781 ctccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct gttggtatct
      841 cggctcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc
      901 cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggaaa gacacgtaaa
      961 aacgccactg gcagcagcca ttggtaaccg ggttagcaga gcgagattta taagttggta
     1021 acagagttct tgaagtatca gcctgattct ggctacacta gaagaacaag ttttggtggt
     1081 ctgcgctctg cttaagccag attacctggt tagataatct gccaggatta gctaaccttt
     1141 gaaaaaccac ctgccagggt ggtttttctt tatgtagaga ttatgctttt aataagcacg
     1201 cagtcaagga ttacaatctc ttataattta atgtattttt ccagatctac attctctaat
     1261 gcatcagata taaaagactg tatgtcttta agttgaggtt tatcctctaa aagatcatct
     1321 acattcagtt tcgaactaat ataggaagag acctttgcaa cccaatacgg atcactcatc
     1381 gcaacaactt taccatcaat ctcttcagcc atattaacta ttctacttct atcaccaata
     1441 acgtcaacaa taaccattgt gcttatatta tgcatcactc cgccaatatc atccattcgt
     1501 ctaaatctag atactttatc caaacttatt tctgtgttac ccctaccaat aaaaccaatg
     1561 tcaaccctaa tcgccttccc attaaaaaca agagtagcat cagactccct gtcatcagct
     1621 cttgttgaaa gagtaaaaca tttagcattt aacccttctt caattttttc tttatattca
     1681 aaacccatta ttgtaaataa agaaccgagt attagctttt caaaatattt accatgaaga
     1741 gatttctcag atcccctaat agttaaagtt tgcgaaccaa gagataaaat aatatagcaa
     1801 aaatcttcta aagacacctt ttgcccacca atagatatct ctccaatttt atcttcatac
     1861 ccgtttttta ttttaagtat ttcttcttgc gtccttaaag caagtctatc aaaaccatcc
     1921 ccatgctcat ctcttaaaac attttgggtc tgtttatttg tcatcataac catccactcg
     1981 agaacaggtt gattagactt aacataagac ttgttcgata atgcattttt tgcatagaga
     2041 taaagctgct ttggcgttat cccttctttc attttatcca caaaaaagtc aaaaaaagag
     2101 agattgcttt ctaacaatct agtacgagtt agtatttcag tgaattcgcg aacattttta
     2161 cctgttaaaa catcataaac aaccttttta aaaacatccg ttccgaactt atctaaaaca
     2221 tcattttttg aaattttcgc caacgctatg agttcgttag ggaaacaatt tttatccttg
     2281 aaattcatat cctcaccatg gacatagtaa aaatgagatg ctaagatagc aggttgtatg
     2341 gtaacagatc gatagttagg aaaaatgaca gttaaaaaca attacttaaa cagaggttat
     2401 ttggtaacct ctacgactca ggcgaaaaaa atagcaaagt tgcacctaga gaaattagac
     2461 ttagctgata aattttcctt tgggttacct gaagtcgatg atcggtacca tgtatggcgt
     2521 gtaccattag tagcgacagg ccacaggatt ggtgaaatag ttataaattc aaaaacgtca
     2581 actattgatt ataagaaaag ttcgaagtct ccatttctta ttaagaaagc aatggaggtt
     2641 gtccataccc caaaaaaggt aaaaaaagaa aaaaaaatca tatcaaagtc accattaaat
     2701 aacatgttac tacaaggcaa ctgcgcggag accttgaaaa aattacctga tgaatcagtg
     2761 aacttagtat tcacatcacc gccatattac aatgccaaac cagagtattc cgaatatcat
     2821 acatatgatg aatacctctc tctattgcgt tcagtaataa aagagtgcca tagagtttta
     2881 agcgaaggtc gttttttcgt catcaatgtc tcgcccgttt taataagaag ggcgtcacgg
     2941 aatgaagcat caaaaagaat agctgttcct tttgacttgc acaggttatt tatagaagaa
     3001 ggctatgaat tcatagatga tatacattgg gttaaaccag aaggagctgg ctgggcttta
     3061 ggtagaggcc gtcgattcgc agctgaccgc aatccgttgc aatataaacc agtaccagta
     3121 actgagtaca ttcttgttta cagaaaaaaa actgataaat taatagattg gaacataaga
     3181 aaccatcata gcaaagagga tgtttttgac tcaaaaatcg gcgacgatta tgaaaagaca
     3241 aacctatgga aaataaatcc atctcgtaac agaaaacatc ctgctacatt tccatacggt
     3301 ctggcagaaa gagttataaa atactattct ttcaaaaatg atgttatttt agatcctttt
     3361 gctggatcgg gaacaacagc aaaagcagca attgatttag gcagaagatt tgtgatgtgt
     3421 gagatatcaa agcagtatat tgatctgatc atagaaggaa ccatgctagg tggtgattta
     3481 aaaatcataa attaatcaaa ctttactgtg gtaaaagccg ccttaaggcg gcttatttac
     3541 gcgtcaacat cagccacatt gtcgaattta ccataatccc ttaattgtac gcaccgccaa
     3601 aacgcgttca gcgcgatcac agcagcagac aggtaaaaat ggcaacaaac cacccgaaaa
     3661 actgccgcaa tcgcgcctga taaattttaa ccgcatgaat acctatgcaa ccagatggta
     3721 cagaccacat tagcctgtct taatccactt aacctgccat ttttcatggt ttcaccatcc
     3781 cagcgaaggg ccatccagcg tgcgttcctg tatttccggc tgacgctccc gttccaggga
     3841 taacacatgt tcgcgctcct gtatcagccg ttcctctctt atctccagtt ctcgctgtat
     3901 aactggctca agcgttctgt ctgctcgctc aagtgctgca cctgctgact caactgcatg
     3961 acccgctcgt tcagcatcgc gttgtcccgt tgcgtaagcg aaaacatctt ctgcaattcc
     4021 acgaaggcgc tctcccattc gctcagccgc tgcatatagt cctgttgcag ctgctctaag
     4081 gcgttcagca aatgtgtttc cagctctgtc actctgtgtc actccttcag atgtacccac
     4141 tctttcccct gaaagggaat cacctccgct gatttcccgt acggaaggac aaggaatttc
     4201 ctgttcccgt cctgcacaaa ctccacgccc catgtcttcg cgttcagttt ctgcaatgtc
     4261 tcttcctgct tcctgatttc ttccaggttc gcctgtatcc tccctccaag ataccagagc
     4321 gtcccgccac tcgctgtaaa caggagaaag actatcccca gtaacatcat gcccgtattc
     4381 cctgccagct ttaacacgtc cttcctgtgc tgcatcatcg cctctttcac cccttcccgg
     4441 tgtttttcca gcgatttctc tgtcgaggct gtgaacaggg ctatagcgtc tctgattttc
     4501 gtctcgtttg aggtcacagc ctcgctgaca gactcgccga gcctcctgaa ctcgttgttc
     4561 agcattttct ctgtagattc ggctctctct ttcagctttt tctcgaactc cgcgcccgtc
     4621 tgtaaaagat tgctcataaa atgctccttt cagcctgata ttcctcccgc cgttcgggtc
     4681 tgcaatgctg atactgcttc gcgtcaccct gaccacttca atccctgcct ccgtgagcgc
     4741 ctgaatcaca tcctgacggc cttttatctc cccgacatga taaagagcgt ctatcccgcg
     4801 tgtgacgctc tctgcaagcg cctgtttcgt tttcggcagg ttatcaggga gagtcagtat
     4861 ccggcggttc tccggggcgt tggggtcatg cagcccgtaa tggtgattaa ccagcgtctg
     4921 ccaggcatca attctcggcc tgtctgcccg gtcgtagtac ggctggaggc gttttccgct
     4981 ctgtagctcc atgttcggaa tgacaaaatt cagctcaagc cgtcccttgt cctggtgctc
     5041 cacccacagg atgctgtact gatttttttc gagaccgggc atcagtacac gctcaaagct
     5101 cgccatcact ttttcacgtc ctcccggcgg cagctccttc tccgcgaacg acagaacacc
     5161 tgacgtgtat ttcttcgcaa atggcgtggc atcgatgagt tcccggactt cttccggatt
     5221 accctgaagc accgttgccc cttcccggtt acgctccctt cccagcaggt aatcaaccgg
     5281 accactgcca ccaccttttc ccctagcatg aaatttaact atcatcccgc gtcccctgtt
     5341 ccctgacggc cagacgcagc cggcgcagct catccccgat ggccatcagt gcggccacta
     5401 cctgaacccg gtcaccggaa gaccactgtc cgctgttcac cttcctcgct gtctgattca
     5461 ggttattccc gatggcggcc agctgacgca gtaacggcgg tgccagtgtc ggcagcttcc
     5521 cggaacgggc aaccggctca cccaggcaga cccgccgcat ccataccgcc agttgtttac
     5581 cctcacagcg ttccagtaac cgggcatgtt catcatcagt aacccgtatc gtgagcatcc
     5641 tctcgcgttt catcggtatc attaccccca tgaacagaaa tccccc
//
