LOCUS       NZ_CP041285             4145 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain 54 plasmid p54-p2, complete sequence.
ACCESSION   NZ_CP041285
VERSION     NZ_CP041285.1
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 4145)
  AUTHORS   Dong,N., Chen,S. and Zhang,R.
  TITLE     Complete genome sequence of E coli strain 54
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  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
            CP041285.1.
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="54"
                     /host="cow"
                     /db_xref="taxon:562"
                     /plasmid="p54-p2"
                     /geo_loc_name="China"
                     /collection_date="2018"
     gene            complement(34..>216)
                     /locus_tag="FK536_RS22410"
                     /old_locus_tag="FK536_22620"
                     /pseudo=""
     CDS             complement(34..>216)
                     /locus_tag="FK536_RS22410"
                     /old_locus_tag="FK536_22620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            <213..455
                     /locus_tag="FK536_RS22415"
                     /old_locus_tag="FK536_22625"
                     /pseudo=""
     CDS             <213..455
                     /locus_tag="FK536_RS22415"
                     /old_locus_tag="FK536_22625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            complement(493..1635)
                     /gene="wzz(fepE)"
                     /locus_tag="FK536_RS22420"
                     /old_locus_tag="FK536_22630"
     CDS             complement(493..1635)
                     /gene="wzz(fepE)"
                     /locus_tag="FK536_RS22420"
                     /old_locus_tag="FK536_22630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            1830..2213
                     /locus_tag="FK536_RS22425"
                     /old_locus_tag="FK536_22635"
     CDS             1830..2213
                     /locus_tag="FK536_RS22425"
                     /old_locus_tag="FK536_22635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003117291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5/IS1182 family transposase"
                     /protein_id="WP_021544857.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLHESQHPGQGGA
                     PISHHQATVRLRESQIQGVAEKR"
                     /name="IS5/IS1182 family transposase"
     gene            2176..2292
                     /locus_tag="FK536_RS23345"
     CDS             2176..2292
                     /locus_tag="FK536_RS23345"
                     /inference="COORDINATES: protein motif:HMM:NF013752.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001407452.1"
                     /translation="MKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="hypothetical protein"
     gene            complement(<2441..2572)
                     /locus_tag="FK536_RS23350"
                     /old_locus_tag="FK536_22640"
                     /pseudo=""
     CDS             complement(<2441..2572)
                     /locus_tag="FK536_RS23350"
                     /old_locus_tag="FK536_22640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(2880..2993)
                     /locus_tag="FK536_RS22435"
                     /old_locus_tag="FK536_22650"
     CDS             complement(2880..2993)
                     /locus_tag="FK536_RS22435"
                     /old_locus_tag="FK536_22650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(2877..3262)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 aaaaaaagcc ccgcagggct tttttgctat gagttagcca tattttcttg cgaatttttc
       61 atcggaatcg catagataaa taataaactc aataaacgcg atgatcgcgg gtatgaatgt
      121 ccagcaaaaa attagataca ggaatccctg tcctatttta cctaagtaaa atttatgtac
      181 gccaaatcca ccaaggaaga atgctaagaa agatgatggc ggtggaggtc aattttgagc
      241 agggtgcgat tggcccgatg cacaatcacc cgcatgaaca gcttacctat gtgctctccg
      301 gggagttcga gtttacgata ggtgaagaaa agcagatcgt gacggcgggc gatacgctct
      361 ataaagcgcc gcacgtgatg cacggctgca tttgcctgaa gcccggcacc cttctggata
      421 cctttacgcc ggtgcgcgac gatttcctga aataaaaaaa ggcgctgaat cagcgccttt
      481 ttaatatcgt cgttactctg ttgctggcgt tacggccgtt atcggctctg gcaacggatt
      541 acgcgagagc attgcctcac gcagcagcac gctgccgcag gcaaacaggc cgcccagaat
      601 ccctgccagc agcacaatca gggctttgcc cggaccgtct tttttcaccg gcagtgacgg
      661 tgaaagctga tacctgaagg gttcaagctt cacgtcttcc acggacagtt tttgcaactg
      721 agtcagatag tattcacggt tctggaaatc cgcattcagc tcggccacgt ccttcagatt
      781 cttttcaatc tgcagctttt gcgcaatacc gtcagcaccc agcgccacgg agtagtcagg
      841 atcgtctttt accgcctgtc cgttgctgta aaccggcttc ttaatgcctg ccgcgttcgc
      901 cacttccagc gaatagttga ggcgctgcag gttggtgttg tggatattgg tcagacgcac
      961 gcgatccagc tccagctgct gctgaacgac tttcgttttc agcgtgatct ggttacggat
     1021 attttccatc gtctcctgct caacaatgcg ggagatatag ttgatgtaac cttccagaac
     1081 cgtctgcgcg tctcccgccg tcggggcggt aaagctcagc gtccatgagg tatacggcgc
     1141 tttgtctgcg tctttaacct gcgtgttatc tgtcgctttc attttctcag caatattcac
     1201 caccgcgcga tgcagctcca gcgggtctac ctcggtgcct tccagctgag acatcacgta
     1261 cggggaggtt ttcatgtact cttcgagcag cgactgcgac tgaaactttt tgatgaacag
     1321 gttaaacacg tctccacggc tcaccttcgc gtcgacgtcc agcacctgca gcgtcaccat
     1381 catctggcgc agcgtgttcc actgcgtctg ctcggccggc gtgatcacgg ctttactggt
     1441 ccatttttgc gggattaaaa acgcaatggc caaccctact acggcgaacg ccaggacgat
     1501 cgtcacaata cgttttttgg ctgccagaag tacgtctaac aaccccagga gatctatctc
     1561 tttggtgctt accgccggag tggcataacg gggaaaatcg aggtccgtgt ttttcttgaa
     1621 atccatcgct gacataaccg ttcttctttt tggagcgcag taaatttctg cctgattggt
     1681 tgcagtggtc ggatgataca agaaagtaag aataatctga acgccagatt gatctatctg
     1741 tagaccgact atcagattta gggaaggtgc gaacaagtcc ctgatatgag atcatgtttg
     1801 tcatctggag ccatggaaca gggttcatca tgagtcatca acttaccttc gccgacagtg
     1861 aattcagcag taagcgccgt cagaccagaa aagagatttt cttgtcccgc atggagcaga
     1921 ttctgccatg gcaaaacatg gtggaagtca tcgagccgtt ttaccccaag gctggtaatg
     1981 gccggcgacc ttatccgctg gaaaccatgc tacgcattca ctgcatgcag cattggtaca
     2041 acctgagcga tggcgcgatc gaagatgctc tgtacgaaat cgcctccatg cgtctgtttg
     2101 cccggttaca tgaaagccag catccgggcc aaggtggagc acccatttcg catcatcaag
     2161 cgacagttcg gcttcgtgaa agccagatac aaggggttgc tgaaaaacga taaccaactg
     2221 gcgatgttat tcacgctggc caacctgttt cgggcggacc aaatgatacg tcagtgggag
     2281 agatctcact aaaaactggg aataacgcct taaatggcga agaaacggtc taaataggct
     2341 gattcaaggc atttacggga gaaaaaaatc ggctcaaaca tgaagaaatg aaatgactga
     2401 gtcaaccgag aagaatttcc ccgcttattc gcaccttccc taatagcgcg gctgcgattc
     2461 tacttttttc acctgaacct gaagaggcgt ttgtggctcc gcagtgtggg catgactttg
     2521 ctgtttcgtg tatttccttg ccgcatcctc ggcagtaaac cattgaactc attttttatc
     2581 ctcgagctta tttttagttg ggatgcataa tatccgatgt tttataacga tatgcatcct
     2641 atatgctcgg gtgggataga tttccattat ggtgaaggat cttcttgaga tcctttctgt
     2701 agcgtcgtaa tctcttgctc agtaaacgaa aaaaccgccc agcaaggcgg tttttcgaag
     2761 gttctcagag ctgcaactct ttgaaccgtg gtaactggct tatgaggagc gcagtaacca
     2821 aatctgttct ttcagtttag ccttaacagg cgcataactt caagactaac tcctctaaat
     2881 cagttaccag tggctgctgc cagtggcgct ttgtcgtgtc tttccggctt ggactcaagt
     2941 cgatagttac cggagaagac gcagcggtcg gactgaacgg ggggttcgtg catacagtcc
     3001 agcttggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag ataaacgcgg
     3061 ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga
     3121 gccaccaggg ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca ccactgattt
     3181 gagcgtcaga ttctgtgatg cttgtcaggg gggcggagcc tatggaaaac cggcaacgcc
     3241 gcggcctttt cttttgcctc tcgatcctct ctcattgcct gtgccttaat gtctccgttc
     3301 cctccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaat
     3361 atccccggac ttatcttcgg caccgtacgc gccagtgctg cattttttaa tacgatgcag
     3421 gatagggcta acgccgcaaa gtgacgtcac ctgacgttcc tggattacaa aggttaaagc
     3481 agcggacagg aaatgttttg tgcccacagc tatgctggct tattcacaaa acagcgggac
     3541 aagatgtgtt tttggagtac cgccggcccg ctaaagactc ctggttagct cccgcatgtt
     3601 tgctatcttt ttgctaccat tttgctactt ttttgctatc tccagagtct tctggtcttt
     3661 cggttgctat ccttttgcta cttttttgct atcaaaatgc tacctctccc ttcttgcaat
     3721 aaatgaccaa ggcacgttag cgatgtatac atcgccgcgc cgcaagggtg ccccttccga
     3781 atcccgttca tcactgcgtg ctgattcatc cacgttaaat ccgaccccct tagcaataaa
     3841 tccagccatg cctgacggcc tggccaacgc ctcacggccg cacagtaaac tgcacacccg
     3901 tgaggcgtta ttcgtgaggt tcagtggtgc ttttgggcgt ccagccggat tttagccgct
     3961 aaaatcccgg ccatgcatgt gtgtgcatag ccatgcagac gcgccagaat catcaggcgc
     4021 gttttttcac gatataggca cagggaagtg tcggaaacag gcaggaagac ccagaaacgc
     4081 cctgagagcc tctcaggcgg tgcacgcaac ggatgttatg gtaaatctgc ctcacagact
     4141 ggtac
//
