LOCUS       NZ_CP127304             4644 bp    DNA     linear   CON 20-JUN-2023
DEFINITION  Escherichia coli strain C51 plasmid pC5109, complete sequence.
ACCESSION   NZ_CP127304
VERSION     NZ_CP127304.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35637912
            Assembly: GCF_030285565.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4644)
  AUTHORS   Mihailovskaya,V., Sutormin,D., Trofimova,A., Mamontov,V.,
            Kuznetsova,M. and Severinov,K.
  TITLE     Complete Genome Sequences of Three Commensal and Two Avian
            Pathogenic Escherichia coli Strains Isolated from Farm Animals in
            Russia
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4644)
  AUTHORS   Mihailovskaya,V., Sutormin,D., Trofimova,A., Mamontov,V.,
            Kuznetsova,M. and Severinov,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2023) Laboratory of Metagenome Analysis, Skolkovo
            Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1,
            Moscow 121205, Russia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2023
            Assembly Method                   :: Flye v. 2.9.1
            Assembly Name                     :: E_coli_C51
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 170x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 16:50:00
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,401
            CDSs (total)                      :: 5,279
            Genes (coding)                    :: 4,916
            CDSs (with protein)               :: 4,916
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 363
            CDSs (without protein)            :: 363
            Pseudo Genes (ambiguous residues) :: 0 of 363
            Pseudo Genes (frameshifted)       :: 204 of 363
            Pseudo Genes (incomplete)         :: 170 of 363
            Pseudo Genes (internal stop)      :: 64 of 363
            Pseudo Genes (multiple problems)  :: 67 of 363
            Pseudo Genes (short protein)      :: 2 of 363
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP127304.1.
            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..4644
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="C51"
                     /isolation_source="feces"
                     /host="Bos taurus"
                     /db_xref="taxon:562"
                     /plasmid="pC5109"
                     /geo_loc_name="Russia: Perm krai"
                     /collection_date="2020-07"
                     /collected_by="Kuznetsova Marina, Mihailovskaya Valentina"
     gene            complement(<1..991)
                     /gene="traU"
                     /locus_tag="QRM70_RS00005"
                     /old_locus_tag="QRM70_00005"
     CDS             complement(<1..991)
                     /gene="traU"
                     /locus_tag="QRM70_RS00005"
                     /old_locus_tag="QRM70_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_490576.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer pilus assembly protein TraU"
                     /protein_id="WP_000830839.1"
                     /translation="MKRSLWLLMLFLLAGHVPAASADSACEGRFVNPITDICWSCIFPL
                     SLGSIKVSQGKVPDTANPSMPIQICPAPPPLFRRIGLAIGYWEPMALTDVTRSPGCMVN
                     LGFSLPAFGKTAQGTAKKDEKQVNGAFYHVHWYKYPLTYWLNIITSLGCLEGGDLDIAY
                     LSEIDPTWTDSSLTTILNPEAVIFANPIAQGACAADAIASAFNMPLDVLFWCAGSQGSM
                     YPFNGWVSNESSPLQSSLLVSERMAFKLHRQGMIMETIGKNNAVCNEYPSPILPKERWR
                     YQMVNMYPDSGQCHPFGRSVTRWETGKNPPNTKKNFGYLMWRKRNCVFL"
                     /name="traU"
     gene            complement(988..1620)
                     /gene="traW"
                     /locus_tag="QRM70_RS00010"
                     /old_locus_tag="QRM70_00010"
     CDS             complement(988..1620)
                     /gene="traW"
                     /locus_tag="QRM70_RS00010"
                     /old_locus_tag="QRM70_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_490575.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type-F conjugative transfer system protein TraW"
                     /protein_id="WP_001203720.1"
                     /translation="MRCRGLIALLIWGQSVAAADLGTWGDLWPVKEPDMLTVIMQRLTA
                     LEQSGEMGRKMDAFKERVIRNSLRPPAVPGIGRTEKYGSRLFDPSVRLAADIRDNEGRV
                     FARQGEVMNPLQYVPFNQTLYFINGDDPAQVAWMKRQTPPTLESKIILVQGSIPEMQKS
                     LDSRVYFDQNGVLCQRLGIDQVPARVSAVPGDRFLKVEFIPAEEGRK"
                     /name="traW"
     gene            complement(1617..2003)
                     /gene="trbI"
                     /locus_tag="QRM70_RS00015"
                     /old_locus_tag="QRM70_00015"
     CDS             complement(1617..2003)
                     /gene="trbI"
                     /locus_tag="QRM70_RS00015"
                     /old_locus_tag="QRM70_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_490574.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type-F conjugative transfer system protein TrbI"
                     /protein_id="WP_000214082.1"
                     /translation="MTTTQKTTDVTAPRRSHWWWTVPGCLAMVLLNAAISYGIVRLNAP
                     VTAAFNMKQTVDAFFDSASQKQLSEAQSKALSARFNTALEASLQAWQQKHHAVILVSPA
                     VVQGAPDITREIQQDIARRMRAEP"
                     /name="trbI"
     gene            complement(2000..4629)
                     /gene="traC"
                     /locus_tag="QRM70_RS00020"
                     /old_locus_tag="QRM70_00020"
                     /pseudo=""
     CDS             complement(2000..4629)
                     /gene="traC"
                     /locus_tag="QRM70_RS00020"
                     /old_locus_tag="QRM70_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001064255.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein TraC"
                     /name="traC"
     Typing          complement(36..991)
                     /name="MPF_F"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="99.06"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(992..1620)
                     /name="MPF_F"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="99.524"
                     /coverage="97.0"
                     /evalue="8.54e-138"
     Typing          complement(2013..3583)
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="93.893"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acaggaagac acagttacgt ttacgccaca tcaggtagcc gaagtttttc tttgtattgg
       61 gcggattttt cccggtttcc cagcgggtca cactgcgccc gaacgggtgg cactgtccgc
      121 tgtccgggta catattcacc atctggtaac gccagcgttc tttgggcagg attggggacg
      181 gatattcatt acagacggcg ttatttttcc cgatggtttc cataatcatg ccctgacggt
      241 gcagcttgaa cgccatgcgt tcactgacca gcagggagga ctgcaacgga ctggactcat
      301 tactcaccca gccattgaac gggtacatac tgccctgcga accggcacac cagaacagaa
      361 catcgagagg catattaaag gcgctggcaa tggcatctgc tgcacaggcc ccctgtgcta
      421 tcggattggc aaagatgaca gcttccggat tgagaatggt ggtcaggctg ctgtccgtcc
      481 aggtggggtc gatttcagaa agataagcga tatccaggtc accaccttcc agacagccca
      541 gcgatgtgat gatgttaagc cagtacgtca gcgggtattt gtaccagtga acgtgataga
      601 acgccccgtt cacctgcttc tcatcctttt tcgccgttcc ctgtgccgtt ttaccaaaag
      661 ccggcaggct gaagcccagg ttaaccatgc atcccggtga tcgggtgacg tccgtcagcg
      721 ccatcggctc ccagtaacca atggccagcc cgatacgcct gaacagcggc ggcggtgccg
      781 gacaaatctg aatgggcatc gacgggttcg ccgtgtcggg gaccttaccc tgactgactt
      841 tgatactgcc cagcgagagc gggaaaatac agctccagca gatatccgtg atcgggttta
      901 caaaacgccc ctcacaggca gaatccgcag acgctgcagg gacatgaccg gcgagaagga
      961 ataacatcag cagccacagg cttcgcttca ttttctgccc tcctctgccg gaataaattc
     1021 caccttcagg aagcgatcgc cgggaacggc gctcacccgt gccgggacct gatcaatgcc
     1081 gaggcgctgg cagagcacac cgttctggtc aaagtaaaca cggctgtcca gagacttctg
     1141 catctccggg atactgccct gcacgaggat aattttgctc tccagtgtgg gcggcgtctg
     1201 gcgtttcatc caggccacct gcgccggatc atcgccattg atgaaataca gcgtctggtt
     1261 aaaaggaaca tactgcagcg gattcatcac ttcaccctga cgggcaaaca cccgcccttc
     1321 gttatcccgg atatccgcag ccagtctgac ggacgggtca aacaaccggc tgccgtattt
     1381 ctccgtgcgt ccgataccgg gcacggcagg gggccgcaga ctgttgcgga tcacccgctc
     1441 cttaaaggca tccattttcc ggcccatctc accggactgc tccagtgccg tcaggcgctg
     1501 catgatcacc gtcagcatgt ccggctcctt taccggccac agatcgcccc aggtgccaag
     1561 atcggcggcg gccacactct gcccccatat cagcagggca atcagccccc ggcatctcat
     1621 ggctccgccc tcattcgccg ggcgatatcc tgctggattt cccgggtgat atccggagcc
     1681 ccctgtacca cggcaggcga caccagaatg accgcgtggt gtttctgctg ccacgcctgc
     1741 aggctggctt ccagtgccgt gttaaaacgc gctgaaaggg cttttgactg tgcttctgac
     1801 agttgtttct gactggcgct gtcaaaaaac gcatccacgg tctgtttcat gttgaaggcg
     1861 gcagtcaccg gtgcgttcag tctgacaatg ccgtaactga tggctgcgtt cagtaacacc
     1921 attgccaggc atcccggcac cgtccaccac cagtggctgc gtcggggggc tgtaacatcc
     1981 gtcgtttttt gcgttgtggt catgcaacac tcctgtattt ctcatgttct tccagccagg
     2041 cttccagcga agccatctcc ggccctgact tcttccacgc cagctgccac accgcctcat
     2101 gaatactcag cccctcttta cgtttctgct gcacaaactc aaaatccggg ccgtcagagc
     2161 tgtacatggc gcggcttaac gggtccacaa acaggcggtg ccaggaggaa tggttttcca
     2221 cctgcagcag gaaggaactg aaccactggt ctttggccgc accaaactta ccaatcatgt
     2281 cgcgctgcag tggctggaac tggtccggat acagctggtt gtattttgcg aactccttcg
     2341 cactctgttt gaggataatt ttgtaggagg agttacccca tgccgcacgg gccgcactgg
     2401 aggccttgtc agagtcaaag tcgacgatgt tctgtgtgat ggtgatatag gcaccggtat
     2461 gacggcgggc ggtacggtaa cctttctcaa taaactcacc gaccttgcga tttttgaagt
     2521 ccagcagacg ccagccttca tcaataacgt tcagtttctt gaggttacgc ggcgtgcggt
     2581 acatcctgtt ctcgatgtag ataatcaggg agaacatcac cgcaaccagc agtgacggac
     2641 ggtcttccag tccgcccagc tccagcacca ccattttcgc atcatcccgc agggacggct
     2701 catcggagtt aaaatactgg ccgtaagtgc cgttggcagt gtactggtca agcagcacaa
     2761 tcatttcgtc cagacggctg cggatggtcg gtgacccggc atactgctcg ctgtcactgg
     2821 cgtttttcag gaaatccacc acgtcatcaa tacgtgccct gttctctttg gccagccagg
     2881 aggccctgac cgcctgcagc agcagacctt catgcacttc atccaggtta ccgttggggc
     2941 tggccatcac tgacaactgg tcacggacac gctccgctga ctggtcaata tcggtgatgt
     3001 tcgcaaacgg gttaaaacgc agggtttcac cgtccagata tacgccaccc atgttctcac
     3061 acagggactt gtagccatcc cccatgtcga acaccacggc aaagcccccg gagtccagca
     3121 cgctgcggat aagtggctgt atcagcccgg ttttaccggc cccggaggtg ccacagaccg
     3181 ccatgttgta gttggtgtta ttcatccccc ggaagaaaat atcgataaac gccagctggt
     3241 tacggtaggt gggtgccagc agacctgccg gtgtcagggg gttatccgcc actaacggca
     3301 tcaggttggc aacattaaag ctctctgcgc gctgaaccac tccggcctct ttcagctgtt
     3361 taaacaaccc tttcccggcc ataaagggca gacaggtcag gaaattgcgc atgtggttaa
     3421 agcgcggtga aatcagctca aaaccgtttt tacggaagct gttcaggatg tcctgctcca
     3481 cttccagcgc cgtttcattg ttgtccttgc agaatgctgt gatgttgagg aagtaggaca
     3541 cgacagaaga ctgaccggag cccagacgct gacgcagttc ccccactcct tcgcctcttt
     3601 ctccacggac ggaaaccatt tggcatagga ggtcttcgac tttttctcca ggtccatgta
     3661 cttcaggttg gcttcgctgt gggttttcac ctggtcttcc accaccagag tcagcgtcag
     3721 gatgaacgga caggagatgg acagttccgg gttcagcagg ttgctgtagt tgtcggccat
     3781 attccacagg aaggcgattt ccgggttacg ggccagatgg aaattcagga tacgggccgt
     3841 gctgttcctg ccgttctcac gcaggcccag cgtcaggtaa tcagcccgga cattcaggtc
     3901 aaaactgtcc tccacacact gataattcag atcagaatac gggtccagct gacgtctttt
     3961 cgggtacagg gagtccgggt tatggttaat catctccccg acaatatcga taaaggcctg
     4021 tgcatccacc gtctgtgtgg cgatactggc cccctgtaac gacgcccgga tgattttcac
     4081 caggttttcc atttccagaa tgtcagcccg gctttttttc ttcgagggag aacagtacga
     4141 gataaatacc cggtaatggc gcagggtcag gggcagattc atcccctccg gcagcggaaa
     4201 ctgtgtcgct gccgctttca tataataggc ccgggtaatg gcgttaaacc gttcagcctg
     4261 ttcacctgac caggagaact cacgcagccc gtactcaatc ctgtcaccaa ccagctgact
     4321 ggacatcaga tggatacaca acggaatacc gcgcggcagt ttggtgcgca gcatgtgatc
     4381 gagtgcctcc acaatggact tattcgcccc attgatggga atggcttcca gcataaagcc
     4441 catcgtggtg tcattcatga acagaccgga ttcctggttg taatcacggt acggcagcag
     4501 acggctgaac tgcgggaagc tcatttcgcc cagaacttca ttggcctttg cggattcgtc
     4561 aggcagtttc agtgctgtga cgagggagtt aaccgcctga gtgacggctt cctcaagtgg
     4621 gttattcaca tgaattcctt agtt
//
