LOCUS       NZ_CP018966             4087 bp    DNA     circular CON 13-JUN-2024
DEFINITION  Escherichia coli strain Ecol_542 plasmid pEC542_4, complete
            sequence.
ACCESSION   NZ_CP018966
VERSION     NZ_CP018966.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN05511186
            Assembly: GCF_002012025.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4087)
  AUTHORS   Stoesser et al,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2016) Microbiology (Research), University of
            Oxford, Headley Way, Oxford OX3 9DU, United Kingdom (Great Britain)
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. unspecified
            Genome Coverage                   :: XX
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002012025.1-RS_2024_06_13
            Annotation Date                   :: 06/13/2024 03:40:06
            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)                     :: 5,434
            CDSs (total)                      :: 5,314
            Genes (coding)                    :: 5,082
            CDSs (with protein)               :: 5,082
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 85 of 232
            Pseudo Genes (incomplete)         :: 166 of 232
            Pseudo Genes (internal stop)      :: 47 of 232
            Pseudo Genes (multiple problems)  :: 55 of 232
            Pseudo Genes (short protein)      :: 1 of 232
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP018966.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ecol_542"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC542_4"
                     /geo_loc_name="Viet Nam: Ho Chi Minh City"
                     /lat_lon="10.82 N 106.62 E"
                     /collection_date="2011"
                     /collected_by="Merck Study for Monitoring of Antimicrobial
                     Resistance Trends (SMART)"
     gene            complement(join(3873..4087,1..1945))
                     /gene="mobQ"
                     /locus_tag="BE966_RS00005"
                     /old_locus_tag="BE966_00005"
     CDS             complement(join(3873..4087,1..1945))
                     /gene="mobQ"
                     /locus_tag="BE966_RS00005"
                     /old_locus_tag="BE966_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_001029343.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            2124..2378
                     /gene="mobC"
                     /locus_tag="BE966_RS00010"
                     /old_locus_tag="BE966_00010"
     CDS             2124..2378
                     /gene="mobC"
                     /locus_tag="BE966_RS00010"
                     /old_locus_tag="BE966_00010"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2910..3617
                     /locus_tag="BE966_RS00020"
                     /old_locus_tag="BE966_00020"
     CDS             2910..3617
                     /locus_tag="BE966_RS00020"
                     /old_locus_tag="BE966_00020"
                     /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"
     Typing          complement(1588..1946)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1947..2123
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2911..3617
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..2032)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.852"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 catcgtgatt tacggcaaca ccataccctg cataccgtaa ccccttatcg gtcagtgcac
       61 tgatgaccag ctggctgtta tcggctgagg gaacggcaaa cgcgggatac agcgtaccat
      121 taagccggac aacaccgccc agagagtcat ccacgcccat gaccagcaaa agctgaagct
      181 ggcgggtttc ccggtcgaca gaactcatta ccggcatcag cgtcggtagc agacgtccct
      241 gcgtaaaatc caccttcctt gctgccagtg atggcatggc tggctggcgg tcttctccaa
      301 gacagaaaga ctccggccat gtcttcggct ggcggagatt gcgggtatat tgcggccatg
      361 tctggcaaac ctgcgtcaga agttgctcaa aggtcgcaga ggaataaaca cgttgcagtg
      421 gtggatgttg accgatttcg cttcggtcac agatataacc actcctgtca cgcattaaat
      481 caacacgctc aaagattctg gtgcggtatt tctccagctc gttcccccag agcgtgtatt
      541 ctccgttccg gttgtgaagc agaaggtaac aggtcatttc cccgttacca ggcatggggg
      601 cctcgccata ccccgtaacg actgcgctca gtacccctga atccataacg gcattgtcat
      661 ttttcctgag ctgttccgct cgtcgctccg cgcgactacg ttctgtatcc tcctgctcct
      721 tccggcgcaa ttcctcttca cgtttaagca actggactct gagagctgca aggccggatg
      781 ccccccactg ctgccactgt ttttcaaatg ccgtctgact cgcgggaatg tcctgtttct
      841 ccaccttccg gtaatgctgt cgcaattttt ccatttgctg gctcagcgac tggatttttc
      901 cctgttcgct acggtattcc ggtgccgccc attgcatcag gggaatacgg gaaaaaccgg
      961 acgaaaacgg cgatgatttt ttcaggctgg cagcatggct catcgcttcc tttcgttcgg
     1021 tgttcagctc ttcccagcgt ctgcgcgtcg cctgcatatc tgccatcatc gacatggcat
     1081 tactggtgag tttccatgcc gcattactgt ccttcggcaa cgcttcgatg atgtcacgta
     1141 gtgtgtacga agttgcgttg tcaggaagca cgatattcag aaggtcagcc acacggcggg
     1201 caggctctgt cagcccgctg tttctgagtt cggtacggga aatctgtatt tccaggttaa
     1261 gtctgttaat cagacgattc tgttcgccgc gttctgtttc gataccgcgt gtttccatcg
     1321 cacaggcaga ctttccgagg tgaataccag gcgttttctc aagcccctgt cgctcgtatg
     1381 aacgatggtc tatctcttcc tgataaccgg cgttcgccag tgccctgttc gcatggtcag
     1441 cccatgatgc acgccacgtc tcggcatgtg tccggtcgtt ccagtccctg acctttccac
     1501 cgaatccagc aggtccgaca gctctcgtgg tcagcatgat gtgcgcatgg ggatttgttt
     1561 tatccatgtg atggaacgcc acatcagcaa tcatgccctg actgacaaag ttttctctga
     1621 caaaggcgag aacggtttcc cgtgcggcat cctgcggtag ttcgcggggg atggcgagtt
     1681 caatttcccg cgcaagttgt gagttcttcc ggcgttcggc cttctcaacg gcattccaga
     1741 gttcggcacg gttcgtacac caggcagggg ctgtcgcggg agtcagaatc acagcttcag
     1801 ccacaccgct tttgcgggtg tagtcgtgag tcagtccggt acgctcatca agcatcagtg
     1861 aaccggaacg ataggcagca gaagcaacgg cgctgtagcc gctgtttctg gagatgattt
     1921 tcatgctgag atgataaatc gccatttctg ccgtaatgcc tttttgtggt tttctttcag
     1981 ccccgcaggg cgcacacaat cgaaacggag tggagattgt ataagtgcgc acttcgtgat
     2041 tttccgtgca ttatgccagc tcagttttta aactaccagt gacgcgctaa aatgcgattt
     2101 ttcatcgcgc acggagttac atcatgagca gaacactcga acagaagatt gctgatgctg
     2161 aggccagatt acagcgcctg aaggcgaaga gcaggagtct ggacacagcg cagaaggtca
     2221 ttgtgggtgc agcattgctg gcaaaggtca gaaagccgga ggaggtgcag ttgcgtgcct
     2281 ggttactcca gttcctgaag gcagaggtga cacgacaggc tgatgtgacg cgcatactgc
     2341 cgctgattaa cgagctggaa gcgctgccag gacagtgatt gtatcgtccg ctcgccgcag
     2401 tcccagcgac cgagcgttag cgagcgagtg ggcgaggaag cggaagtgaa tccgtcgcct
     2461 gattgagcac atacgcacgg tttttcggga ggtgatatgc gctgaacccg catgaatact
     2521 ggatttccac agggttggag ggggtgtatt cggaacttgc aattctgctt ttttgcaacg
     2581 cattgttttt attggttttt tgttttcagc actccaagtt atccacaggc tcgtcgttaa
     2641 gtttttagat cttgttttta agatcttgtt tttaatactt gttttagcgc caaaattcct
     2701 tatagaaaac aaaatgttac aacgctatag gtgatatgat ttaaggtaaa ggtgatataa
     2761 tttaaggtgc ttgggtgagg taatttaagg taaaggtgag gagatttaag gtaatattca
     2821 caggaaaatg gggggtgaaa atataattgc tcaccaatgc taaaggtgat aggtttttat
     2881 ttcacctcat ttttggcctg gtggttaaaa tgacatcaaa ccctctgata gcctataagt
     2941 ccaatgcgct ggttgaggcc agttacaagc taactttaca agaacagcgt ttcttattgc
     3001 tctgcataag ccgacttaac tccggtactg acgtagcttc acctgaattg caaaagacaa
     3061 tgaccattac agctgcggaa tattttgatt cattccctga tatggggcgg aaaaatgccg
     3121 aggttcagct acaggaagcg atcgatcgtt tgtgggacag gtcgatcatt ctcaaggacg
     3181 acgagaagcg cgaggagttc cgctggattc agtatcgggc acagtacgcg aggggagagg
     3241 ggaaagcaca aatcactttt tctgacgcgg taatgcctta tctgacacag ttgaaggggc
     3301 aattcaccag agtcgtcatt aaaaatattt ctaatttatc aagaagttac agcataagaa
     3361 tatacgaaat tctccagcaa ttccgcagta ctggggaacg tattatcgcc ctcgatgatt
     3421 ttaaatcatc actgatgctt gatggtaaat ataaagattt caaaacgtta aacagggatc
     3481 taataaaacc ctgtgttgac gaactgaaca aaaaaagcga cctggctgta acggttgaga
     3541 cgatcaaaaa ggggcgcacg gttgtagccc tgcattttcg cttcaaggaa gacaaacaga
     3601 tcaagatgac gatctagaat cgattttaag gcacctaaaa cgctccctgc tgcgtttttt
     3661 ttgtgttagt agtgcgaagg tactattgaa gtgaaaaatt gcgtcaaaag cgctctaatg
     3721 cagcgaaaaa agaaccccca tttttcgggg gcggaaaaac aaaactatgc ttgcattatg
     3781 tgtgtgcttc ttgcattcat ccctgtcgat gaacatcgaa gaacatcgac gaacataaca
     3841 cgatgttaaa caaaacaaaa tattgttcac attcactgtg accaaccgcg atcatgtctc
     3901 ctctcggtgg cgtgtgttcg tgcatcttcc tcgcgccgcc attcgtccca ggtacgatta
     3961 aaacccagcg agcggaacag atgatccggc tgtttttctg gtgtgttgac ggcagcaaaa
     4021 agcggtgcct cacgggtttt cagatgaaac tccataagtt ccggcgcagg tgatatgtgg
     4081 ctgtctg
//
