LOCUS       NZ_CP010162             4075 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli strain H1 plasmid B, complete sequence.
ACCESSION   NZ_CP010162
VERSION     NZ_CP010162.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03252429
            Assembly: GCF_001900775.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4075)
  AUTHORS   Jiang,J., Xu,Z., Zhou,Y., Zhao,H. and Leung,F.C.C.
  TITLE     Vertical and Horizontal Evolutionary Story implied from E. coli
            complete genomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4075)
  AUTHORS   Jiang,J., Xu,Z., Zhou,Y., Zhao,H. and Leung,F.C.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-NOV-2014) Bioinformatics Center, Nanjing Agricultural
            University, F214, South Wing, Science & Experiment Building, 1
            Weigang, Xuanwu District, Nanjing, Jiangsu 210095, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Newbler v. 2.7
            Genome Coverage                   :: 30-80x
            Sequencing Technology :: Illumina Miseq; Roche 454 GS Junior
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001900775.1-RS_2024_06_12
            Annotation Date                   :: 06/12/2024 04:18:13
            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)                     :: 4,733
            CDSs (total)                      :: 4,607
            Genes (coding)                    :: 4,399
            CDSs (with protein)               :: 4,399
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 63 of 208
            Pseudo Genes (incomplete)         :: 147 of 208
            Pseudo Genes (internal stop)      :: 44 of 208
            Pseudo Genes (multiple problems)  :: 38 of 208
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP010162.1.
            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..4075
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="H1"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="B"
                     /collection_date="2014"
     gene            577..1695
                     /gene="wzz(fepE)"
                     /locus_tag="RG44_RS25950"
                     /old_locus_tag="RG44_24070"
     CDS             577..1695
                     /gene="wzz(fepE)"
                     /locus_tag="RG44_RS25950"
                     /old_locus_tag="RG44_24070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243311.1"
                     /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_024191316.1"
                     /translation="MFSMKISKISDEHFSNYNMLPNGNEEIDLFDLIRVLWAAKIKIVG
                     VILFFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAF
                     ALFIKKFQSVNSLNEYMRSSPYVMEIIKKKNISALELHRAIVGLSENMKSVDDNASKKN
                     DKSSLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNELEVKTNVEKEIL
                     ALDEIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATK
                     LNIKKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAI
                     IVILSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            2632..2781
                     /locus_tag="RG44_RS27155"
     CDS             2632..2781
                     /locus_tag="RG44_RS27155"
                     /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_001515742.1"
                     /translation="MPSEYDEQPDATDALFPGEYDLFDLMAHVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            3250..3441
                     /locus_tag="RG44_RS25960"
                     /old_locus_tag="RG44_24075"
     CDS             3250..3441
                     /locus_tag="RG44_RS25960"
                     /old_locus_tag="RG44_24075"
                     /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_000166329.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCETLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3441..3842
                     /locus_tag="RG44_RS25965"
                     /old_locus_tag="RG44_24080"
     CDS             3441..3842
                     /locus_tag="RG44_RS25965"
                     /old_locus_tag="RG44_24080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_000135006.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVTRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          2425..2639
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.091"
                     /coverage="100.0"
                     /evalue="3.48e-51"
     Typing          complement(1916..2444)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.545"
                     /coverage="89.0"
                     /evalue="1.2e-144"
ORIGIN
        1 gactcgtcat agagtcatcg acgactcact taagactatc agtaacttat gatgacttga
       61 ctctagagtt gaatcgtcat tttggtgttt ttttgacctt tacgactcta gagtcaagtc
      121 acgagtcgaa tcgccggtga attgtctggt gagtcgtccg gcgacttgcc ataacgtgat
      181 tgccggccgt cgacgaaccc gattcctgat cgtgctgaaa accggttttc cggctgcgcc
      241 ggcaacgctt cacggccacg caataaattg cgtccccgtt caccgttttc ggataggaag
      301 aacgccggaa acaggactta ccctggctga atggcgtgaa ttttcgcgct atgcacttgc
      361 gtgcatactc atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg
      421 gtttgttgcc tgttttaccg gtttcccgtc agaaacgccc tgaggccgtt ttagtggtgc
      481 gtacaattaa aatgttatgt taaatgtctg ctgaatggtt tttaggattt ttcctaacat
      541 atgatagaat aaaaaaacca tatgttaata tattgtattt tttcaatgaa aatctcaaag
      601 atatctgacg aacatttttc taattacaac atgttgccga atggtaatga agaaattgac
      661 ctttttgact tgattagagt tttatgggca gcaaaaataa aaattgttgg ggtgattcta
      721 ttttttgctt gtattggctt tcttgtttct tttgttttgc cacaaaaatg gactagttct
      781 gctgtggtta ctcctgctga gtctgttcaa tggagtgaat taaataagga gctttccaag
      841 cttcatgttc tgggagtgga ttttgatatc aatcgtgata gcgcatttgc tctgtttatt
      901 aagaaatttc agtccgttaa ttcgttgaat gagtatatga gatcatctcc ttatgttatg
      961 gagataatta aaaagaagaa cattagcgct ctagaactgc atcgtgcaat tgttgggttg
     1021 agtgaaaata tgaagtcggt tgatgataat gccagtaaga aaaacgacaa gtcatcattg
     1081 tatgtatcat ggactctgag ttttactgct ccaacaagta aagaagctca cgatgtgttg
     1141 tctgggtata ttaattatgt ttcttccctt gttgtaaggg atttgatgga agatataaga
     1201 aatgaactag aagttaaaac taatgttgaa aaagaaattc ttgcactgga tgagataaaa
     1261 attagaaacc agctgaatgc agatattcga cgcctcaatt attcactgga ggttgctaat
     1321 gcggctggaa taaaaaaacc tgtatacagc aatggtcaga ttatgaagga tgatccagat
     1381 tttcctgtgg ctctcggttc tgatggtata gcaactaaat tgaacatcaa aaaatcaatc
     1441 aaggatgttt cggaattgag tggggagttg cgaaatcgtc aatatgttgt gaatcaattg
     1501 gttgtggcga aagtggggga tgttgatttt atgccgtttc agtatcaatt gagcccaacg
     1561 ttaccggtca gaaaggatgg gccaagtaat gccataattg taattctttc ttctgtcatt
     1621 ggagggatgc ttgcatgtgg ctatatactt ttacgtcatg ccatggaggc cagaaagatg
     1681 agtgtgattg agtaaaagtt gtgctgatgc atcattttat aagcaacttt tataaaaagt
     1741 tcaaaggatc ttcttgagat cattccctta cagccgtagt cttctactct agaaaacgaa
     1801 aaaaccacct ggggaggtgg tttttcgaag gttcagtaag ttggggaact tctgaaccgt
     1861 ggtaacagtc ttgtgcgaga catgtcacca aatctgtcct tctagtgtag cctcagtaag
     1921 gctgccactt caagaactct caatacatct ctcgcacatc ctgtttacca gtggccgctg
     1981 ccaatggcgt taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     2041 cgcagcggtc gggctgaacg gggggttctt gcatacagcc cagcttggag cgaactgtct
     2101 aaacggaacg gggcgtggtg atttaggtaa agcttccacc actacacgga tgccgcagga
     2161 cgggaacagg agagcgcaag agggagccac cagggggaaa cgcctggtat ctttatagtc
     2221 ctgtcgggtt tcgccaccac tgatttgagc gtcagatttc gtgatgcttg tcaggggggc
     2281 ggagcctatg gaaaaacggc tttgccgcgg ccttatcgta tccctgttaa gtttcttcct
     2341 ggcatccacc aggaaataaa tttccgcccc attcgtaagc ctgcaccgct cgccgcagcc
     2401 gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga atatcacctg aaccagcatc
     2461 ttctcctgac gccggtaagc ctcatttcac tcctgccaca tgaagcactt tggcaaatca
     2521 ccacttcggt ttaaaatatt tagccagtat gcactccgct agcgctacgt gactggttca
     2581 gggctgcgcc ccgaaacccg ctaacacccc tcagctactg gatatcacac catgccatct
     2641 gagtatgatg aacaaccgga tgcgactgat gctctgtttc ccggcgaata tgaccttttt
     2701 gacttaatgg ctcatgttac tgaagagaac ctgcacgccc cggtggattc tggcccgcct
     2761 gtcggccggg aagcgttata gctttttcgc tggccagcgt acatgtaata cgctggtatt
     2821 acatgttatt tgtttatttt catgttgtta cagatgattg taatacgttg cgtattacgc
     2881 taatacacga aataactcca tttttttcat ttaattcatg cagttgcgat aaaaatcgcg
     2941 gctgcgttag gtgtatgacc atttaagggg caaaaaatta tcattctggc tgggtgatct
     3001 gcgcaggtta aggatcatcg gcgacgaaaa agcgtcttta actgcttcgt tcatgcaagc
     3061 atgaacggat tatttttcca gactacagga agactacaaa agttgatgat ttaatcctgc
     3121 gttttagtgc gatgactaca gataaactac aaaataacta caggataacc tcagatccgt
     3181 tctctgaacc attcgtacat ccgaccccct taccggttta tactgagcac tgatgctctg
     3241 agggccctta tgacgaaaca acagaaaaca gcgctgaaca tggctaaatt catccagaat
     3301 cagtctctgc tcctgctgga gaagcttaac gagcttgatc tcgatgttga ggcggacctt
     3361 tgtgagacac tccacgatga tgcggagcat cttttccgta cactgtcctc gagattggat
     3421 gcattacagg atggtaactg atggccagag tatctattag tgaggctgcc cgactgacgg
     3481 gtaagagtag aacaacactg cacaggttaa ttaaagcagg tgacctgtcc acctgtagcg
     3541 gtgaacgcaa tgcaaaaatg gtagatactt cagagctttt acgtgtcttt ggtccctttg
     3601 aacaaccgaa gggtgaacac cattctggac aggtctctga acagcgtgat acagcctctg
     3661 ctgaccagag tgaacaggtg actcgtcatc tgaaacagga gattgaacac ctgaacacct
     3721 tacttttgtc caaggattcg cacattgaca gcctgaaaca ggctatgctc cttcttgaaa
     3781 atcaccaggc aaaattaact gaatccccgg cgccatggtg gaaattctgg aaaaaatcct
     3841 gaccccgtca tgcttcagtt ttcctctccg gccatcccgg ggagttcctg aaccttctca
     3901 aaaatcgtca gatctctgaa cgctcctcac cactaaaaat acccacaccc tacgcaaaat
     3961 taaaattttg aagataactc attaatatca gttagttgtg ggttattaaa ttacgcagta
     4021 ttactttctg taaggtgaat ccaagtcgtc ggcgattcgt gtacgacttg ctgac
//
