LOCUS       NZ_CP041283             4072 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain 54 plasmid p54-p3, complete sequence.
ACCESSION   NZ_CP041283
VERSION     NZ_CP041283.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12158158
            Assembly: GCF_012278675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Dong,N., Chen,S. and Zhang,R.
  TITLE     Complete genome sequence of E coli strain 54
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Dong,N., Chen,S. and Zhang,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-JUN-2019) Department of Applied Biology and Chemical
            Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon
            000000, Hong Kong
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: unicycler v. 0.3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology             :: Nanopore MinION; illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 01:53:45
            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)                     :: 4,660
            CDSs (total)                      :: 4,542
            Genes (coding)                    :: 4,334
            CDSs (with protein)               :: 4,334
            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)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 59 of 208
            Pseudo Genes (incomplete)         :: 142 of 208
            Pseudo Genes (internal stop)      :: 36 of 208
            Pseudo Genes (multiple problems)  :: 29 of 208
            Pseudo Genes (short protein)      :: 4 of 208
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041283.1.
            Bacteria and source DNA available from State Key Lab of
            Chirosciences, Department of Applied Biology and Chemical
            Technology, The Hong Kong Polytechnic University, Hung Hom,
            Kowloon, Hong Kong.
            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="54"
                     /host="cow"
                     /db_xref="taxon:562"
                     /plasmid="p54-p3"
                     /geo_loc_name="China"
                     /collection_date="2018"
     gene            77..331
                     /gene="mobC"
                     /locus_tag="FK536_RS00005"
                     /old_locus_tag="FK536_00005"
     CDS             77..331
                     /gene="mobC"
                     /locus_tag="FK536_RS00005"
                     /old_locus_tag="FK536_00005"
                     /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"
     gene            861..1568
                     /locus_tag="FK536_RS00010"
                     /old_locus_tag="FK536_00015"
     CDS             861..1568
                     /locus_tag="FK536_RS00010"
                     /old_locus_tag="FK536_00015"
                     /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(1823..3970)
                     /gene="mobQ"
                     /locus_tag="FK536_RS00015"
                     /old_locus_tag="FK536_00020"
     CDS             complement(1823..3970)
                     /gene="mobQ"
                     /locus_tag="FK536_RS00015"
                     /old_locus_tag="FK536_00020"
                     /inference="COORDINATES: protein motif:HMM:NF015354.2"
                     /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"
     Typing          complement(3613..3971)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.722"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3972..4072
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="9.94e-46"
     Typing          862..1568
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.294"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1827..4057)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcattatgcc agctcagttt ttaaactacc agtgacgcgc taaaatgcga tttttcatcg
       61 cgcacggagt tacatcatga gcagaacgct cgaacagaag attgctgatg ctgaggcgag
      121 attacagcgc ctgaaggcga agagccggag cctggacaca gcgcagaagg ttgttgtggg
      181 tgctgcattg ctggcaaagg tcagaaagcc ggaggaggtg cagttgcgtg cctggttact
      241 ccagttcctg aaggcagagg tgacacgaca ggctgatgtg acgcgcatac tgccgctgat
      301 taacgagctg gaggcgctgc cagaacagtg attgtatcgt ccgctcgccg cagcccagcg
      361 accgagcgtt agcgagcgag tgggcgagga agcggaagtg aatcagtcgc catgttgagc
      421 acatacgcac ggtttttcga caggtgatat gcgctgaacc cgcatgaata ctggatttcc
      481 acagggttgg agggggggta ttcggaatct ccaatcctga ttttttgcaa cacattgttt
      541 ttattgggtt tttattttca gcactccaag ttatccacag gctcgccgtt aagtttttag
      601 atcttgtttt taatacttgt ttttaatact tgttttaggg tcgaaattcc tgattaaaaa
      661 caatgcgtta cacgtgtata ggtggggaaa tttaaggtaa aggtgatata atttaaggtt
      721 cttgggtgag gtaatttaag gtaaaggtga ggagatttaa ggtaatattc acagaaaaat
      781 ggggggtgga aatataattg ctcaccaatg ctaaaggtga taggttttta tctcacctca
      841 tctttggcct ggtggttaaa atgacatcaa accctctgat agcctataag tccaatgcgc
      901 tggttgaggc cagttacaag ctaactttac aagaacagcg tttcttattg ctctgcataa
      961 gccgacttaa ctccggtact gacgtagctt cacctgaatt gcaaaagaca atgaccatta
     1021 cagctgcgga atattttgat tcattccctg atatggggcg gaaaaatgcc gaggttcagc
     1081 tacaggaagc gatcgatcgt ttgtgggaca ggtcgatcat tctcaaggac gacgagaagc
     1141 gcgaggagtt ccgctggatt cagtatcggg cacagtacgc gaggggagag gggaaagcac
     1201 aaatcacttt ttctgacgcg gtaatgcctt atctgacaca gttgaagggg caattcacca
     1261 gagttgttat taaaaatatc tccaatttat caagaagtta cagcataaga atatacgaga
     1321 ttctccagca attccgcagt actggggaac gtattatcgc cctcgatgat tttaaatcat
     1381 cactgatgct tgatggtaaa tataaagatt tcaaaacgtt aaacagggat ctaataaaac
     1441 cctgtgttga cgaactgaac aaaaaaagcg acctggctgt aacggttgag acgatcaaaa
     1501 aggggcgcac ggttgtagcc ctgcattttc gcttcaagga agacaaacag atcaagatga
     1561 cgatctagaa tcgattttaa ggcacctaaa acgctctctg ttgcgttttt tccatgagag
     1621 gtatgcgatg gtactactgg tgagataaaa ttgcttcata atcgattcta tggcgttcaa
     1681 aaaaaagaac ccccaactta gtgggggcgg gaaaacgata aagttggatt tgtgcaatct
     1741 gtgtgcatct gacattcatc cagttacgat gaatgtcaga gaacataaca cgatgtaaaa
     1801 caaaacaaaa tactatcagc agttaccgtg aacagtcgcg atcatttttc ttcccggaga
     1861 cacgtgttcg tgcatgctcc tcgcgccgcc attcatccca ggtgtgatta aagcccagtg
     1921 aacggaacag atgatccggc tgtttttctg gtgtgttgac ggcagcaaaa agcggtgtct
     1981 cgcgggtttt aagatgaaac gccataagtt ccggtgcagg tgaaatgtgg ttgtctgcat
     2041 cgtgatttac ggcaacacca tatcctgcat atcgtaaccc cttatcggtc agcgcactga
     2101 tgaccagatg cctgttatcg gcggagggga cagcaaacgc gggatacagc gaaccattaa
     2161 gccggacaac accgcccaga gagtcatcca cgcccatgac cagcaaaagc tgaagttgtc
     2221 ggttttcccg gtcgacagaa ctcattaccg gcatcagcgt cggtggcaga cgtccctgcg
     2281 taaaatccac cctccttgcc accggtgatg gcatggctgg ctggcggttt tctccaagac
     2341 agaaagactc cggccatgtc ttcggctggc ggagattgcg ggtatgttgc ggccatgtct
     2401 ggcaaacctg cgtcagaagt tgctcaaagg tcgcagagga ataaacacgt tgcagtggtg
     2461 gatgttgacc gatttcgctt cggtcacaga tataaccact cctgtcacgc attaaatcaa
     2521 cactctcaaa gatcctggtg cggtatttct ccagctcgtt cccccagagc gtatattctc
     2581 cgttccggtt gtgaagcaga aggtaacagg tcatttcccc gttaccaggc atgggagcct
     2641 cgccatatcc cgtaacgact gctctcagca cccctgaatc cataacggca ttgtcatttt
     2701 tcctgagctg ctccgcgcga ctacgttctg tatcctccag ctccttccgg cgcaattcct
     2761 cttcacgttt aagcaactgg gatctgagag ctgcaaggcc ggattccccc cactgctgcc
     2821 actgtttttc aaatgccgtc tgactcgcgg gaatgtcctg tttctccacc ttccggtaat
     2881 gctgtcgcaa tttttccatt tgctggctca gagactggat ttttccctgc tcactacggt
     2941 attccggtgc agcccattgc atcaggggaa tacgggaaaa accggacgaa aacggcgatg
     3001 attttttcag gctggcagca tggctcatcg cttcctttcg ttcggtgttc agctcttccc
     3061 agcgtctgcg tgtcgcctgc atatctgcca tcatcgacat ggcgttactg gtgagtttcc
     3121 atgccgcgtt actgtccttc ggcaacgctt cgatgatgtc acgtagtgtg tacgaagttg
     3181 cgttgtcagg aagcccgatc ttcagaaggt cagccacacg gcgggcaggc tctgtcagcc
     3241 cgctgttcct gagttcggtg cgggaaatct gtatttccag gttaagcctg ttaatcagac
     3301 gattctgttc gccgcgttct gtttcgatac cgcgtgtttc catcgcacag gcagactttc
     3361 cgaggtgaat accaggcgtt ttctcaagcc cctgtcgctc gtatgaacga tggtctatct
     3421 cttcctgata accggcgttc gccagtgccc tgtttgcatg gtcagcccat gatgcccgcc
     3481 acgtctcggc atgtgtccgg tcgttccagt ccctgacctt tccgctgaac ccagcaggtc
     3541 cgatagccct cgtggtcagc atgatgtgcg catggggatt tgttttatcc atgtgatgga
     3601 acgccacatc agcaatcatg ccctgactga caaagttttc tctgacaaag gcgagaacgg
     3661 tttcccgggc ggcatcctgc ggcagttcgt gggggatggc gagttcaatt tcccgcgcaa
     3721 gttgtgagtt cttccggcgt tcggccttct caacggcatt ccagagttcg gcacggttcg
     3781 tacaccaggc aggggcggtg gcgggggtca gaatcacagc ctcagccaca ccgcttttgc
     3841 gggtgtagtc gtgagtcagt ccggtacgct catcaagcat cagtgaaccg gaacgatagg
     3901 cagcggaagc tacggcgctg tagccgctgc ttctggagat aattttcatg ctgagatgat
     3961 aaatcgccat ttctgccgta atgccttttt gtagttttct ttcagccccg cagggcgcac
     4021 acaatcgaaa cggagtggag attgtataag tgcgcacttc gtgatttgcc gt
//
