LOCUS       NZ_CP041116             4825 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain ECCTRSRTH03 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP041116
VERSION     NZ_CP041116.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07450616
            Assembly: GCF_002246595.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4825)
  AUTHORS   Fouts,D., Sutton,G., Nguyen,K., White,R., D'Souza,R. and
            Thamlikitkul,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2019) Bioinformatics, JCVI, 9605 Medical Center
            Drive, Suite 150, Rockville, MD 20850, USA
REFERENCE   2  (bases 1 to 4825)
  AUTHORS   Fouts,D., Sutton,G., Nguyen,K., White,R., D'Souza,R. and
            Thamlikitkul,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2019) Bioinformatics, JCVI, 9605 Medical Center
            Drive, Suite 150, Rockville, MD 20850, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 23-MAY-2019
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: ECCTRSRTH03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: NA
            Genome Coverage                   :: 150.12x
            Sequencing Technology :: Illumina NextSeq 500, Oxford Nanopore
            MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002246595.2-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 03:02:23
            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)                     :: 4,934
            CDSs (total)                      :: 4,822
            Genes (coding)                    :: 4,583
            CDSs (with protein)               :: 4,583
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 78
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 74 of 239
            Pseudo Genes (incomplete)         :: 168 of 239
            Pseudo Genes (internal stop)      :: 35 of 239
            Pseudo Genes (multiple problems)  :: 37 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041116.1.
            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..4825
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ECCTRSRTH03"
                     /isolation_source="Rectal swab"
                     /host="Swine"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="Thailand: Nakhon Pathom"
                     /lat_lon="13.8199 N 100.0622 E"
                     /collection_date="2016-08-01"
     gene            complement(64..213)
                     /locus_tag="CI675_RS25010"
     CDS             complement(64..213)
                     /locus_tag="CI675_RS25010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_017880354.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            655..768
                     /locus_tag="CI675_RS25620"
                     /old_locus_tag="CI675_0024660"
     CDS             655..768
                     /locus_tag="CI675_RS25620"
                     /old_locus_tag="CI675_0024660"
                     /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_073511950.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHANAPLAAATGN"
                     /name="replication initiation protein"
     gene            1504..2931
                     /gene="wbaP"
                     /locus_tag="CI675_RS24665"
                     /old_locus_tag="CI675_0024665"
     CDS             1504..2931
                     /gene="wbaP"
                     /locus_tag="CI675_RS24665"
                     /old_locus_tag="CI675_0024665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014230067.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA];
                     GO:0005886 - plasma membrane [Evidence IEA]"
                     /GO_function="GO:0016740 - transferase activity [Evidence
                     IEA]"
                     /GO_process="GO:0000271 - polysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="undecaprenyl-phosphate galactose
                     phosphotransferase WbaP"
                     /protein_id="WP_086642453.1"
                     /translation="MKYIHKNNIVSTSLALSDLVSFAISVGLVLGIHALCTTDFNHTLL
                     MTQLEGWFTLHAIVALGCVGWYSVRLRHYFYRKTFWFELKEILRTLVIFSVFETSIIAF
                     TDWLFPSVIWASIWIVTFILLPTLRMTTKRLLDIVGLWRRETWILGSGKNAVEAFNAVS
                     SERNLGLSVIGFIAGEANSQQVSAIAGIPVINPDAEWLALQDKKTQFIVAVETNQADLR
                     NAWLRNFMIKGYRYVSVIPTLRGMPLDSTDMSFIFSHEVMIFRVQQNLAKVSSRVLKRI
                     FDIFGSLALIVILSPVLIYISRKVKKDGGPAIYGHVRVGKNGKSFKCLKFRSMVVNSKE
                     VLTDVLANDPEARAEWDLNFKLRNDPRVTKIGAFLRRTSLDELPQLFNVLKGEMSLVGP
                     RPIITEELERYNDEVGYYLLSKPGMTGLWQVSGRSDVDYETRIYFDVWYVKNWSIWNDI
                     AILFKTVSVVIKKDGAY"
                     /name="wbaP"
     gene            complement(3795..4217)
                     /locus_tag="CI675_RS24670"
                     /old_locus_tag="CI675_0024670"
     CDS             complement(3795..4217)
                     /locus_tag="CI675_RS24670"
                     /old_locus_tag="CI675_0024670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_086642455.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDAVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKNEPSSPPHSPWWKFWRKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4217..4408)
                     /locus_tag="CI675_RS24675"
                     /old_locus_tag="CI675_0024675"
     CDS             complement(4217..4408)
                     /locus_tag="CI675_RS24675"
                     /old_locus_tag="CI675_0024675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          251..768
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaaaataa agaaataaaa tgtaatactg gcgtattacc acgtacgcga gcaagcgaaa
       61 aagctataac gcttcccggc cgacaggtgg cccggaatcc acaggggcgt gcaggttctc
      121 ttcagtaacc tgcgccatta aatcaaaaag gtcatattcg ccgggaagct gcgtatcagt
      181 cgaatccagt tgttcatcat attcagatgg catggggtga tatccagtag ctgagaggtt
      241 gttagcgggt tgcggggcgt acgggagaaa atggaagccc ggggatatga cgcctcctcg
      301 ctcactcagt cgctgccgct cctgccgttc ggctgcggcg ggcgttacct gcacacggat
      361 aagagcaaag acatacggca tgataagcgg ggcagcaaaa gaatgcgccg ctgccgtttt
      421 tccataggct ccgcccccct gacaagcatc acagaatctg acgctcaaat cagcggtggc
      481 gaaacccgac aggactataa agatcccagg cgtttccccc tggtagctcc ctcgtgcgct
      541 ctcctgttcc tgcctttcgg tttaccgatg tcattccgct gttatggccg cgtttatctc
      601 attccacgcc tgacactcag ttccgggaag gcagttcgct ccaagctgga ctgtatgcac
      661 gaaccccccg ttcagtccga ctgctgcgcc ttatccggta actatcgtct tgagtccaac
      721 ccggaaagac atgcaaatgc gccactggca gcagccactg gtaactgatt tagaggagat
      781 agtcttgaag ttatgcgtca gttaaggcta aactaaacga acagttttgg tgactgcgct
      841 cctctaacta gccagttacc tcggttcaaa gagcgccaac tcttggaacc ttcaaaaaaa
      901 ccgcccgcca aggcggtttt ttcgtttcta gagaaagaga ttacccgcag aaaaagatga
      961 tctcaagaag atcctttgcc agtagcgtca gccttccctc agtagtaagc tgcagtaatg
     1021 cagccaatct attgatactt ccttgcacac caccttaagg acctcttgct gcggcgagca
     1081 ttgcgtgcga aaaatgcgca ccattccccc gaaccagaca cggtgaatcc tctagcgagg
     1141 atttcaccgt gtctactggc tgcaaaaaag ccctctgaca aaagagggct gttatctgat
     1201 ataggcttgt ttagtgccat tcttgcgact agtttttagt ctcgccatat aatcgattga
     1261 tatataatgt tttttgtttt aaataacaac aagtaatcaa caatgaaacg cgaattcaga
     1321 taataagtgc aactctcggt catgtggatg gaattcagtg agcacaagac gatttcggca
     1381 gttcatcccg aagggagcag acctaagtcc tggcacctcg gtggtgcttg ctgagctaag
     1441 acagacgact tagagttgta cttcggactt gcatctgtca tacattttaa aggatgaata
     1501 ttaatgaagt atatacataa aaataacata gtcagtacaa gtctagcgtt gtctgactta
     1561 gtcagttttg ctatttcggt cggcttagta ctaggaatcc atgccttatg tactacagat
     1621 ttcaatcata ccttgctgat gacacagcta gaagggtggt tcacgctgca tgctattgtt
     1681 gctcttggct gtgtcggctg gtattcagtc cgcctgcggc attattttta ccgtaaaaca
     1741 ttttggttcg aattgaaaga aattttgcga accttagtaa ttttctcggt ctttgaaaca
     1801 tcaattattg cttttacaga ctggttattc ccaagtgtca tctgggcttc tatctggatc
     1861 gttacattta tattactgcc aacactgcgc atgacaacta aacgtctact agatatagtt
     1921 ggcctctgga ggcgtgaaac atggattctg ggaagtggaa aaaatgcagt tgaggccttt
     1981 aatgccgtaa gcagcgaacg taatttaggt ttatcagtaa tcggctttat tgctggcgaa
     2041 gctaatagcc aacaagttag tgctatcgca gggatccctg tgattaatcc tgatgctgaa
     2101 tggttagctc tacaggataa gaaaacacaa ttcattgtag cggttgaaac gaaccaagct
     2161 gacttacgca acgcttggtt aagaaatttt atgatcaaag gataccgtta tgtttcagtc
     2221 atccctacat tgcgtggcat gccattagat agcactgata tgtcctttat ttttagccat
     2281 gaggtaatga tcttccgcgt tcaacaaaat ctggctaaag tttcttcaag ggtactaaag
     2341 cggatttttg atatttttgg gtcactcgct cttattgtta ttctttctcc agtcttaatt
     2401 tatattagcc gtaaagtgaa aaaagatggt gggcctgcga tttatggcca cgtgcgagta
     2461 gggaaaaatg gaaaatcttt taaatgcctt aaattccgtt caatggtggt taattcaaag
     2521 gaagtattga ctgatgttct tgccaatgat cctgaagctc gtgctgaatg ggatttaaac
     2581 tttaagttaa ggaatgaccc gcgcgtaact aaaataggtg catttttgcg ccgcacaagt
     2641 ctagatgaac tacctcaatt atttaatgtg ctaaaagggg aaatgagttt agtggggcca
     2701 cggccaatta taactgaaga gcttgaacgt tataatgatg aagtgggtta ctacttactt
     2761 agcaaaccag gaatgacagg cctctggcag gtaagtgggc gcagtgatgt tgactatgaa
     2821 accagaattt attttgacgt ttggtatgtt aaaaattggt caatatggaa tgatattgcg
     2881 atactattta aaacggttag tgtcgtaatt aaaaaggatg gggcttacta aggaaggtgt
     2941 gatttaatcc tcagagattg tacaccattc tgtgtaaata cttttttctc agaagtgacc
     3001 atctaggtgg tcactgaccc cattcactga tgcttttcct cgcatgactt acgtcgctgt
     3061 gacctgctcc ccgttgatta atacaccgcg atgttagtaa tgagtcgtgt atttaggcga
     3121 tagcgcccta tttaccataa tcccttctta cgcgcaccgc gaaaacggcc tcagggcgtt
     3181 tctgacggga aaccggcaaa acaggcaata aaccacccga aaacccgcca gaaacgcgca
     3241 ggctctgttt ttacggcatg catgagtatg cgcgcaagtg catagcgcgg aaattcacgc
     3301 cattcagccg gggtaagtcc tgtttccggc gttcttccca tccgaaaacg gtgaacgggg
     3361 acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag ccggaaaacc ggttttcagc
     3421 acgttcagga atcgggttcg tcgacggccg gcaatcacgt tatggcaagt cgccggacga
     3481 ctcaccacac gattcaccgg cgattcgact ctagagtcaa gtcgtcataa gttactgata
     3541 gtgtggagtg agtcgtcgat gactctatga cgagtcgtag agtcatcgac gacttggatt
     3601 gaccttacag aaggtaatac tgcgtaattt aataacaacc aactaactga tattaatgag
     3661 ttatctgcaa aaatttaatt ttgcgtgggg tgtggatatt tttagtgtga ggagcgttca
     3721 gagatctgac gatttttggg aaggttcacg aacgccccgg catggccgga gaggaaaact
     3781 caagcatggc gggatcagga ttttctccag aatttccacc acggggaatg gggtggtgaa
     3841 gaaggttcgt tcttgtgctc cagaagctgc atagcctgac gaagggaatc aatatgctca
     3901 tctcgagcct taacagcccc tttaagacca tcgttttcag cttcaagtaa agcgattcta
     3961 tgttgtaaat catgtaaacc aacgctgtta atacctgtag attctgcgtc actttttaca
     4021 tcatatttta cagcatcgat tacaccatca agagaaccaa acactctaat aagctctgat
     4081 gtatcaataa ctttaatacc cttcccgtgc tttacaacag aggtgtaact taacttacca
     4141 ctgttaatca tcttgtaaat agtagggcga ctaaccttaa caagccgtgc tgcttcacta
     4201 atagacactc tggccatcag ttaccatcct gtaatgcatc cagtctcgag gacagtgtac
     4261 ggaaaagatg ctccgcatca tcgtggagtt tctcacaaag gtcggcctca gcatcgagat
     4321 caagctcgtt aagcttctcc agcaggagca gagactgatt ctggatgaat ttagccatgt
     4381 tcagcgctgt tttctgttgt ttcgtcataa gggacctcag agcatcagtg ctcagtgtaa
     4441 aaccggtaag ggggtcggat gtacgaatgg ttcagagaac ggatctgagg taatcctgta
     4501 gttattttgt agtttatctg tagtcatcgc actaaaaatc aggattaagt catcagcttt
     4561 tgtagtcttt ctgtagttta cctgtagtcc ggaaaaataa tccgttcatg cgagcatgaa
     4621 cgaggtcgtt aatgacgttt ttttgtcacc gacgcccctt aacctccgca gatcacccgg
     4681 ccagaatgat aatattttgg cccttaaatg gtcatacacc taacgcagcc gcgattttca
     4741 tcgcaactgc atgaattaaa aggtaaaaat tgaaatctcc gtttattttt gtaatacgca
     4801 acgtattaca atcacctgta accac
//
