LOCUS       NZ_CP010156             4600 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli strain D9 plasmid D, complete sequence.
ACCESSION   NZ_CP010156
VERSION     NZ_CP010156.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03252427
            Assembly: GCF_001900715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4600)
  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  JOURNAL   Unpublished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 4600)
  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_001900715.1-RS_2024_06_12
            Annotation Date                   :: 06/12/2024 04:32:36
            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)                     :: 4,734
            CDSs (total)                      :: 4,606
            Genes (coding)                    :: 4,405
            CDSs (with protein)               :: 4,405
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 87 of 201
            Pseudo Genes (incomplete)         :: 108 of 201
            Pseudo Genes (internal stop)      :: 39 of 201
            Pseudo Genes (multiple problems)  :: 30 of 201
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP010156.1.
            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..4600
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="D9"
                     /host="dog"
                     /db_xref="taxon:562"
                     /plasmid="D"
                     /collection_date="2014"
     gene            complement(join(3699..4600,1))
                     /locus_tag="RG42_RS25680"
                     /old_locus_tag="RG42_24180"
     CDS             complement(join(3699..4600,1))
                     /locus_tag="RG42_RS25680"
                     /old_locus_tag="RG42_24180"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5 family transposase"
                     /protein_id="WP_249531280.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAHQHRIHESQHPGQGGAPISH
                     HQATVRLRESQIQGVAEKR"
                     /name="IS5 family transposase"
     gene            196..1338
                     /gene="wzz(fepE)"
                     /locus_tag="RG42_RS26185"
                     /old_locus_tag="RG42_24185"
     CDS             196..1338
                     /gene="wzz(fepE)"
                     /locus_tag="RG42_RS26185"
                     /old_locus_tag="RG42_24185"
                     /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            complement(1376..>1618)
                     /locus_tag="RG42_RS25685"
                     /old_locus_tag="RG42_24190"
                     /pseudo=""
     CDS             complement(1376..>1618)
                     /locus_tag="RG42_RS25685"
                     /old_locus_tag="RG42_24190"
                     /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            <1615..1797
                     /locus_tag="RG42_RS25690"
                     /pseudo=""
     CDS             <1615..1797
                     /locus_tag="RG42_RS25690"
                     /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            2919..3032
                     /locus_tag="RG42_RS25700"
     CDS             2919..3032
                     /locus_tag="RG42_RS25700"
                     /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"
     gene            3340..>3471
                     /locus_tag="RG42_RS27110"
                     /pseudo=""
     CDS             3340..>3471
                     /locus_tag="RG42_RS27110"
                     /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"
     Typing          2648..3036
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.153"
                     /coverage="91.0"
                     /evalue="1.04e-173"
ORIGIN
        1 tgatgaaccc tgttccatgg ctccagatga caaacatgat ctcatatcag ggacttgttc
       61 gcaccttccc taaatctgat agtcggtcta cagatagatc aatctggcgt tcagattatt
      121 cttactttct tgtatcatcc gaccactgca accaatcagg cagaaattta ctgcgctcca
      181 aaaagaagaa cggttatgtc agcgatggat ttcaagaaaa acacggacct cgattttccc
      241 cgttatgcca ctccggcggt aagcaccaaa gagatagatc tcctggggtt gttagacgta
      301 cttctggcag ccaaaaaacg tattgtgacg atcgtcctgg cgttcgccgt agtagggttg
      361 gccattgcgt ttttaatccc gcaaaaatgg accagtaaag ccgtgatcac gccggccgag
      421 cagacgcagt ggaacacgct gcgccagatg atggtgacgc tgcaggtgct ggacgtcgac
      481 gcgaaggtga gccgtggaga cgtgtttaac ctgttcatca aaaagtttca gtcgcagtcg
      541 ctgctcgaag agtacatgaa aacctccccg tacgtgatgt ctcagctgga aggcaccgag
      601 gtagacccgc tggagctgca tcgcgcggtg gtgaatattg ctgagaaaat gaaagcgaca
      661 gataacacgc aggttaaaga cgcagacaaa gcgccgtata cctcatggac gctgagcttt
      721 accgccccga cggcgggaga cgcgcagacg gttctggaag gttacatcaa ctatatctcc
      781 cgcattgttg agcaggagac gatggaaaat atccgtaacc agatcacgct gaaaacgaaa
      841 gtcgttcagc agcagctgga gctggatcgc gtgcgtctga ccaatatcca caacaccaac
      901 ctgcagcgcc tcaactattc gctggaagtg gcgaacgcgg caggcattaa gaagccggtt
      961 tacagcaacg gacaggcggt aaaagacgat cctgactact ccgtggcgct gggtgctgac
     1021 ggtattgcgc aaaagctgca gattgaaaag aatctgaagg acgtggccga gctgaatgcg
     1081 gatttccaga accgtgaata ctatctgact cagttgcaaa aactgtccgt ggaagacgtg
     1141 aagcttgaac ccttcaggta tcagctttca ccgtcactgc cggtgaaaaa agacggtccg
     1201 ggcaaagccc tgattgtgct gctggcaggg attctgggcg gcctgtttgc ctgcggcagc
     1261 gtgctgctgc gtgaggcaat gctctcgcgt aatccgttgc cagagccgat aacggccgta
     1321 acgccagcaa cagagtaacg acgatattaa aaaggcgctg attcagcgcc tttttttatt
     1381 tcaggaaatc gtcgcgcacc ggcgtaaagg tatccagaag ggtgccgggc ttcaggcaaa
     1441 tgcagccgtg catcacgtgc ggcgctttat agagcgtatc gcccgccgtc acgatctgct
     1501 tttcttcacc tatcgtaaac tcgaactccc cggagagcac ataggtaagc tgttcatgcg
     1561 ggtgattgtg catcgggcca atcgcaccct gctcaaaatt gacctccact gccatcatct
     1621 ttcttagcat tcttccttgg tggatttggc gtacataaat tttacttagg taaaatagga
     1681 cagggattcc tgtatctaat tttttgctgg acattcatac ccgcgatcat cgcgtttatt
     1741 gagtttatta tttatctatg cgattccgat gaaaaattcg caagaaaata tggctaactc
     1801 atagcaaaaa agccctgcgg ggcttttttt gtaccagtct gtgaggcaga tttaccataa
     1861 catccgttgc gtgcaccgcc tgagaggctc tcagggcgtt tctgggtctt cctgcctgtt
     1921 tccgacactt ccctgtgcct atatcgtgaa aaaacgcgcc tgatgattct ggcgcgtctg
     1981 catggctatg cacacacatg catggccggg attttagcgg ctaaaatccg gctggacgcc
     2041 caaaagcacc actgaacctc acgaataacg cctcacgggt gtgcagttta ctgtgcggcc
     2101 gtgaggcgtt ggccaggccg tcaggcatgg ctggatttat tgctaagggg gtcggattta
     2161 acgtggatga atcagcacgc agtgatgaac gggattcgga aggggcaccc ttgcggcgcg
     2221 gcgatgtata catcgctaac gtgccttggt catttattgc aagaagggag aggtagcatt
     2281 ttgatagcaa aaaagtagca aaaggatagc aaacatgcgg gagctaacca ggagtcttta
     2341 gcgggccggc ggtactccaa aaacacatct tgtcccgctg ttttgtgaat aagccagcat
     2401 agctgtgggc acaaaacatt tcctgtccgc tgctttaacc tttgtaatcc aggaacgtca
     2461 ggtgacgtca ctttgcggcg ttagccctat cctgcatcgt attaaaaaat gcagcactgg
     2521 cgcgtacggt gccgaagata agtccgggga tattccgctt cctcgctcac tgactcgcta
     2581 cgctcggtcg ttcggctgcg gcgagcggag ggaacggaga cattaaggca caggcaatga
     2641 gagaggatcg agaggcaaaa gaaaaggccg cggcgttgcc ggttttccat aggctccgcc
     2701 cccctgacaa gcatcacaga atctgacgct caaatcagtg gtggcgaaac ccgacaggac
     2761 ttaaagatac caggcgtttc cccctggtgg ctccctcgtg cgctctcctg ttcctgcctt
     2821 tcggtttacc ggtgtcattc cgctgttatg gccgcgttta tctcattcca cgcctgacac
     2881 tcagttccgg gtaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt
     2941 ccgaccgctg cgtcttctcc ggtaactatc gacttgagtc caagccggaa agacacgaca
     3001 aagcgccact ggcagcagcc actggtaact gatttagagg agttagtctt gaagttatgc
     3061 gcctgttaag gctaaactga aagaacagat ttggttactg cgctcctcat aagccagtta
     3121 ccacggttca aagagttgca gctctgagaa ccttcgaaaa accgccttgc tgggcggttt
     3181 tttcgtttac tgagcaagag attacgacgc tacagaaagg atctcaagaa gatccttcac
     3241 cataatggaa atctatccca cccgagcata taggatgcat atcgttataa aacatcggat
     3301 attatgcatc ccaactaaaa ataagctcga ggataaaaaa tgagttcaat ggtttactgc
     3361 cgaggatgcg gcaaggaaat acacgaaaca gcaaagtcat gcccacactg cggagccaca
     3421 aacgcctctt caggttcagg tgaaaaaagt agaatcgcag ccgcgctatt agggaaggtg
     3481 cgaataagcg gggaaattct tctcggttga ctcagtcatt tcatttcttc atgtttgagc
     3541 cgattttttt ctcccgtaaa tgccttgaat cagcctattt agaccgtttc ttcgccattt
     3601 aaggcgttat tcccagtttt tagtgagatc tctcccactg acgtatcatt tggtccgccc
     3661 gaaacaggtt ggccagcgtg aataacatcg ccagttggtt atcgtttttc agcaacccct
     3721 tgtatctggc tttcacgaag ccgaactgtc gcttgatgat gcgaaatggg tgctccacct
     3781 tggcccggat gctggctttc atgtattcga tgttgatggg ccgttttgtt cttgcgtgga
     3841 tgctgtttca aggttcttac cttgccgggg cgctcggcga tcagccagtc cacatccacc
     3901 tcggccagct cctcgcgctg tggcgcccct tggtagccgg catcggctga gacaaattgc
     3961 tcctctccat gcagcagatt acccagctga ttgaggtcat gctcgttggc cgcggtggtg
     4021 actaggctgt gggtcaggcc actcttggca tcgacaccaa tgtgggcctt catgccaaag
     4081 tgccactgat tgcctttctt agtctgatgc atctccggat cgcgttgctg ctctttgttc
     4141 ttggtcgagc tgggtgcctc aatgatggtg gcatcgacca aggtgccttg agtcatcatg
     4201 acgcctgctt cggccagcca gcgattgatg gtcttgaaca attggcgggc cagttgatgc
     4261 tgctccagca ggtggcggaa attcatgatg gtggtgcggt ccggcaaggc gctatccagg
     4321 gataaccggg caaacagacg catggaggcg atttcgtaca gagcatcttc gatcgcgcca
     4381 tcgctcaggt tgtaccaatg ctgcatgcag tgaatgcgta gcatggtttc cagcggataa
     4441 ggtcgccggc cattaccagc cttggggtaa aacggctcga tgacttccac catgttttgc
     4501 catggcagaa tctgctccat gcgggacaag aaaatctctt ttctggtctg acggcgctta
     4561 ctgctgaatt cactgtcggc gaaggtaagt tgatgactca
//
