LOCUS       NZ_CP142048             4989 bp    DNA     circular CON 17-JAN-2024
DEFINITION  Escherichia coli strain L9 plasmid pL9-4, complete sequence.
ACCESSION   NZ_CP142048
VERSION     NZ_CP142048.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39307979
            Assembly: GCF_035666355.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4989)
  AUTHORS   Zhang,L., Tao,M., Li,M. and Liu,J.
  TITLE     Effect of colistin on Escherichia coli biofilm
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4989)
  AUTHORS   Zhang,L., Tao,M., Li,M. and Liu,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JAN-2024) College of Veterinary Medicine, Henan
            Agricultural University, Longzihu District, Zhengzhou, Henan 450046,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 13-JUN-2023
            Assembly Method :: A5-miseeq v. V20152522; CANU v. v1.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 432.0x
            Sequencing Technology             :: Illumina TruSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/17/2024 07:58:43
            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)                     :: 5,001
            CDSs (total)                      :: 4,880
            Genes (coding)                    :: 4,623
            CDSs (with protein)               :: 4,623
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 70 of 257
            Pseudo Genes (incomplete)         :: 192 of 257
            Pseudo Genes (internal stop)      :: 51 of 257
            Pseudo Genes (multiple problems)  :: 51 of 257
            Pseudo Genes (short protein)      :: 4 of 257
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142048.1.
            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..4989
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="L9"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pL9-4"
                     /geo_loc_name="China:Henan"
                     /collection_date="2023-06-13"
     gene            join(4677..4989,1..11)
                     /locus_tag="VPJ62_RS24895"
                     /old_locus_tag="VPJ62_24895"
     CDS             join(4677..4989,1..11)
                     /locus_tag="VPJ62_RS24895"
                     /old_locus_tag="VPJ62_24895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /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_001749507.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="VPJ62_RS24900"
                     /old_locus_tag="VPJ62_24900"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="VPJ62_RS24900"
                     /old_locus_tag="VPJ62_24900"
                     /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            689..1207
                     /locus_tag="VPJ62_RS24905"
                     /old_locus_tag="VPJ62_24905"
     CDS             689..1207
                     /locus_tag="VPJ62_RS24905"
                     /old_locus_tag="VPJ62_24905"
                     /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_058820098.1"
                     /translation="MSNLLQTGAEFEKKLKERAASTEKMLNDEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLKKHREGVNEAMMQHRKDVLKLAGNTGMMLLGIAFLLLTMSG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="VPJ62_RS24910"
                     /old_locus_tag="VPJ62_24910"
     CDS             1214..1447
                     /locus_tag="VPJ62_RS24910"
                     /old_locus_tag="VPJ62_24910"
                     /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_058820099.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMKLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2083..3258
                     /locus_tag="VPJ62_RS24915"
                     /old_locus_tag="VPJ62_24915"
     CDS             2083..3258
                     /locus_tag="VPJ62_RS24915"
                     /old_locus_tag="VPJ62_24915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000893405.1"
                     /GO_function="GO:0005525 - GTP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GTPase"
                     /protein_id="WP_058820100.1"
                     /translation="MLEQVKDFLGDSYNPQTGEFNAEKARAEAEEHKDKFNIILCGATG
                     VGKSSLVNAVFGEEIVKSGVGSPVTQHLEKITVPRKGLVLWDTKGIESKDYENTINQLK
                     NDILHAFNDSSHEDDVPHLGWVCIDSSGARIEERDIEIIGILREKEIPVVVVFTKILGD
                     ESADFIEAAISEINAHHGDFINGRYVKVNSRERKILNISIPVSGLDDLVDISFKALPES
                     KSRARQALKKAQMVKMEERLEAMKDGAKLIVHTSSVAAGVVGATPVPGSDAPLIAGVQS
                     TMIYKINSEFELDITTSASASIISGILGVTAVAQVGKTIVSNVLKFIPGVGSVVGGAIS
                     AATAVGITEAIGHAYIQVLASYYDKTTGKVLLPESVSVVLDLFKKYFTYKK"
                     /name="GTPase"
     gene            complement(3578..3748)
                     /locus_tag="VPJ62_RS24920"
                     /old_locus_tag="VPJ62_24920"
     CDS             complement(3578..3748)
                     /locus_tag="VPJ62_RS24920"
                     /old_locus_tag="VPJ62_24920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_153674799.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLSPLAAAIGNWIRRALMF
                     NQYYRVLEVMA"
                     /name="replication initiation protein"
     gene            complement(4420..4611)
                     /locus_tag="VPJ62_RS24925"
                     /old_locus_tag="VPJ62_24925"
     CDS             complement(4420..4611)
                     /locus_tag="VPJ62_RS24925"
                     /old_locus_tag="VPJ62_24925"
                     /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_016241003.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDSENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4247..4329
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.619"
                     /coverage="97.0"
                     /evalue="3.06e-32"
     Typing          complement(3677..4227)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.29"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1551
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.611"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4648..4988
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.982"
                     /coverage="97.0"
                     /evalue="5.91e-62"
ORIGIN
        1 atgattgtta aatttcatgc caggggaaaa ggcagtggca gtggtccggt tgattacctg
       61 ctgggaaggg agcgtaaccg ggaaggggca acggtgcttc agggtaatcc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtcaggtgt tctgtcgttc
      181 gcggagaagg agctgccgcc gggaggacgt gaaaaagtga tggcgagctt tgagcgcgta
      241 ctgatgcccg gtctcgaaaa gaatcagtac agcatcctgt gggtggagca ccaggacaag
      301 ggacggcttg agctgaattt tgtcattccg aacatggagc tgcagaccgg aaaacgcctc
      361 cagccgtact acgaccgggc agacagaccg agaattgatg cctggcagac gctggttaat
      421 caccattacg ggttgcatga cccgaacgcc ccggagaacc gccggacgct gacactccct
      481 gataacctgc cggaaacgaa acaggcgctt gctgagggtg ttactcgtgg gatagacgca
      541 ctttaccatg ccggagagat aaaagaccgt caggatgtga ttcaggcgct cacagaggcg
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
      661 aggaatatca gactgaaagg agcattttat gagcaatctt ttacagacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgcatc tacagagaaa atgctgaacg acgagttcag
      781 gaggctcggc gaatctgtca gcgaggctgt gacctcaaac gagacgaaaa tcagagacgc
      841 tatagccctg ttcacagcct cgacagagga atcgctgaaa aaacaccggg aaggggtgaa
      901 cgaggcgatg atgcagcaca ggaaggacgt gttaaagctg gcagggaata cgggcatgat
      961 gttactgggg atagcctttc tcctgttaac catgagtggt gggacgctct ggtatctcgg
     1021 cgggaggata caggcgaacc tggaagaaat caggaagcag gaagagacat tgcagaaact
     1081 gaacgcgaag acatggggcg tggagtttgt gcaggacggg aacaggaaat tccttgtcct
     1141 tccgtacggg aaatcagcgg aggtgattcc ctttcagggg aaagagtggg tacatctgaa
     1201 ggagtgacac agagtgacag agctggaaac acatttgctg aacgccttag agcagctgca
     1261 acaggactat atgcagcggc tgagcgaatg ggagagcgcc ttcgtggaat tgcagaagat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag cgggtcatga agttgagtca
     1381 gcaggtgcag cacttgagcg agcagacaga acgcttgagc cagttataca gcgagaactg
     1441 gagataagag aggaacggtt gatacaggag cgcgaacatg ctttatccct ggaacgggaa
     1501 cgccagctgg aaatacagga gcgcacgctg gatggccctt cgctgggatg gtgaaactat
     1561 gaaaaatggc aggttcagca gattgagatg agttaatgtg agctgtacca tttgattgca
     1621 taggtattca tgcggttaaa atttatcagg cgcgatcgcg gcagtttttc gggtggtttg
     1681 ttgttatttt tacctgtctg ctgccgtgat cgcgatgaac atgttttagc agtgcgcata
     1741 aaatggggtt atgttaaatg tgattgatat ctatagatat cagactaact atttattttg
     1801 tacatggtgt taaaattggt aatgattaga atggctatga cttataaatg tttatcatgc
     1861 cattggtgta aaactattcc taaatgtagt gatgctttag ttgatggagt gagcgccttt
     1921 agtcggtgcc caaattgcga ttctattttg gttgatgaaa aaaaagccaa catcattaac
     1981 tcggttattg caaatataat attcaaaata aaatcgtaaa tgattttatt atttgtgtga
     2041 tcgtttgcgt ttttgttggc ttgttattat gtggaggtta aaatgttgga gcaagttaaa
     2101 gattttttag gtgattccta taatccacaa actggtgagt ttaatgcaga aaaggcaagg
     2161 gcagaggctg aggaacataa ggacaaattt aatataattc tttgtggagc tacaggagtt
     2221 ggtaaaagtt ctttggttaa tgcagttttt ggcgaggaga ttgttaagtc aggagtggga
     2281 agtccagtta cccagcattt agaaaaaatc actgttccaa gaaaagggct ggtgttgtgg
     2341 gatacaaaag gtattgagtc aaaagattat gaaaatacca taaatcagtt aaagaatgat
     2401 attcttcatg cattcaatga ctcatctcat gaagacgatg tgcctcattt agggtgggtt
     2461 tgtattgatt cgtcaggtgc aaggatagaa gaaagagata ttgagataat tggtatttta
     2521 agagaaaaag aaatacctgt agttgttgtg tttacaaaaa tacttggcga tgagtctgcc
     2581 gattttatag aggcagccat tagtgaaatt aatgctcatc atggtgattt tattaatggt
     2641 aggtatgtaa aagtaaattc aagagagcgg aaaatactta atatttctat ccctgttagt
     2701 ggtcttgatg atttagtaga tattagtttt aaggcgttac cagaatctaa gagtcgtgcc
     2761 aggcaagcct taaaaaaggc tcaaatggtt aaaatggagg agcgactgga ggccatgaag
     2821 gatggtgcaa aattaattgt tcatacatca tctgtagctg ctggggtggt tggtgcaact
     2881 cctgtgccag gctctgatgc tccgcttatt gctggagtgc agagtacaat gatatacaag
     2941 attaattctg aattcgaact tgatataaca acatcagcat cagcgagtat tattagtggg
     3001 atacttggag ttaccgcggt agcacaggtg ggtaagacca ttgtatctaa tgttttaaaa
     3061 ttcattcctg gtgtgggttc cgttgttggg ggggcaatat cagcagctac agcagttggt
     3121 attactgagg ctattggtca tgcatatatt caagttctgg ctagttatta tgataaaacg
     3181 actgggaaag tcctccttcc agagagtgtt agtgtagttt tggatttgtt taagaaatac
     3241 ttcacatata aaaagtaatt tatgggtgaa tatgttttac cactctggtg ataaatatat
     3301 tcttaatacg gcctccagtt atggatttag ttgatacaac ttaaacgaag ttatgtgaga
     3361 tagaggattg cttcgtttgt atttgcatca agttggcata gatgaaaagg atctccttga
     3421 gatcctttga aaggcgtcgt aatctcttcc gctgtaaacg aaaaaaccgc ctggggaggc
     3481 ggtttttcga aggttaagtc agttggggac tgcttaaccg ggtaactggc ttcagcagag
     3541 cacagatacc aaaactgtcc ttccagtgta gccgtagtta ggccatcact tcaagaactc
     3601 tgtagtactg attaaacatc aatgctctgc gaatccagtt accaatggct gctgccagtg
     3661 gcgataagtc gtgtctttcc gggttggact caagacgata gttaccggat aaggcgcagc
     3721 ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacaccg
     3781 ggccgagata ccaacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg
     3841 cggacaggta tccggtaaac ggcagggtcg gaacaggaga gcgcacgagg gagcttccag
     3901 ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctga cttgagcgtc
     3961 gatttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccatc ggcgtggcct
     4021 ttctctcgcc ctttgtcttt ttgcgcacat gttctttccg gcgctatccc ctgatcctgt
     4081 ggataaccgt attaccgcct ttgagtgagc tgataccgct cgccgcagcc gaacgaccga
     4141 gcgtagcgag tcagtgagcg aggaagcgga agagcacctg aactggcatt ttctccttac
     4201 gcatctgtgc ggtatttcac accgcatatg gcgctgtttt cttacaattc gcactgatgc
     4261 cgcatagtat aagccagtat acactccgct atcgctacgt gactgggtca gggctgcgcc
     4321 ccgacacccc ctaaaacctg ctgacgcgcc ctgacgggct tgtctgctcc cggcatccgc
     4381 tcacagacaa gctgtgaccg tctccgggag ctgcatgtgt cagaggtttt cactgtcatc
     4441 cccgaaacgt gcgaggcaac tgcggtaaag ctcatcggcg tggtcgtgaa gcgattcaca
     4501 gatatctgcc tgttcatccg cgtccagttc gttgagcttc tccagcagcg ttaatgtctg
     4561 gcctctgatg aagcgcgcca tgttaagggc ggttttttcc tgtttagtca ctgatgcctc
     4621 cgtgtaaggg ggattactgt tcgtgggggg taatgatacc gatgaaacgc gagaggatgc
     4681 tcacgatacg ggttactgat gatgaacatg cccggttact ggagcgctgt gagggtaaac
     4741 agctggcggt atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaaac
     4801 tgccgacact ggcaccgccg ttactgcgtc agctggccgc catcgggaat aacctgaatc
     4861 agacggcgag gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg
     4921 ccgcactgat ggccatcgag agagagttgc gcagcttacg gcaggtcgtc agggaacagg
     4981 gagcgcggg
//
