LOCUS       NZ_CP010185             4980 bp    DNA     circular CON 13-JUN-2024
DEFINITION  Escherichia coli strain M3 plasmid B, complete sequence.
ACCESSION   NZ_CP010185
VERSION     NZ_CP010185.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03252440
            Assembly: GCF_001901045.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4980)
  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  JOURNAL   Unpublished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 4980)
  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 :: Il;lumina Miseq; Roche 454 GS Junior
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001901045.1-RS_2024_06_13
            Annotation Date                   :: 06/13/2024 02:40:43
            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)                     :: 5,033
            CDSs (total)                      :: 4,906
            Genes (coding)                    :: 4,706
            CDSs (with protein)               :: 4,706
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 89 of 200
            Pseudo Genes (incomplete)         :: 120 of 200
            Pseudo Genes (internal stop)      :: 44 of 200
            Pseudo Genes (multiple problems)  :: 47 of 200
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP010185.1.
            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..4980
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="M3"
                     /isolation_source="feces"
                     /host="mouse"
                     /db_xref="taxon:562"
                     /plasmid="B"
                     /collection_date="2014"
     gene            join(4663..4980,1..69)
                     /locus_tag="RG55_RS27115"
                     /old_locus_tag="RG55_25565"
     CDS             join(4663..4980,1..69)
                     /locus_tag="RG55_RS27115"
                     /old_locus_tag="RG55_25565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000147848.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WP_249531554.1"
                     /translation="MTGRSRSQFYRDMRAGLVSYRTSQDGRREFETSELIRAYGELKRN
                     ETPERHTAGQAEKPHDQQTERILRELNELKQCLTLMLEDKQAQDTERQRQEAEREQLQN
                     EIAQLRQALEQEKKRGVWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            150..578
                     /locus_tag="RG55_RS27120"
                     /old_locus_tag="RG55_25570"
     CDS             150..578
                     /locus_tag="RG55_RS27120"
                     /old_locus_tag="RG55_25570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000830439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_042089515.1"
                     /translation="MKRSGGTRYMYLSALITVAAALTACTPKTSLEQHTRHYVYASDDG
                     FDPNFYTKKADTTRMMIPFFQQFREMGVKDKAAGVSAETAQQRIKEFHSEEFLQSLRTT
                     TTFAGRKYTNGDMPSPEKMKLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            1413..1604
                     /locus_tag="RG55_RS27130"
                     /old_locus_tag="RG55_25575"
     CDS             1413..1604
                     /locus_tag="RG55_RS27130"
                     /old_locus_tag="RG55_25575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_001401730.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGEAL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2592..2732)
                     /locus_tag="RG55_RS28510"
     CDS             complement(2592..2732)
                     /locus_tag="RG55_RS28510"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_153276082.1"
                     /translation="MKKMFFVGVVIISFCLVACQMNNIKGNSGGSFSSSNSGVGIQVKK
                     S"
                     /name="colicin release lysis protein"
     gene            complement(3126..4352)
                     /locus_tag="RG55_RS27160"
     CDS             complement(3126..4352)
                     /locus_tag="RG55_RS27160"
                     /inference="COORDINATES: protein motif:HMM:NF013211.4"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_073520811.1"
                     /translation="MAKELGGYGPTAGESMGGTGANLNQQGGHNNSGVHWGGGSGHGNN
                     GGQGNTSSSNSTSTVMKPGESYLTPWGDVVINKDGLPVMNGVVMTEDNSSLVDNPLGGV
                     SRVLNSLISDMPSLFTKATGNNHDNNITAVNAVSPETRASDMEKSSKMVSALIDEKQNQ
                     KNQIAAQISEKNKKIEEMKKIFKHHSYHGITDLERDVDELQRKSNQLDADISKLYDYKN
                     TLKSDVDKIKDAVAYTATFYEKVTEKYGEKAELLAKSLADKANGKTIRGVDDALAAFDR
                     YRSSLGDKFNSADRAAIVAGIQALDATNTANSLAKYSKAFGYLGNAIDLADILVELKNA
                     LTTDNWRPVLVKLEIITANRAAVAISAIVFSIITGVPMGIVGFGVLVALAGSFFDEQLV
                     NEINSQLGI"
                     /name="colicin-like pore-forming protein"
     Typing          1763..2307
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.698"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gcccagctca ggcaggcgct ggagcaggaa aagaaacggg gagtctggtc caggttgttc
       61 ggtcgctgaa cgcactcaga gactgatgat aagatagcca tcagataata actcaccgaa
      121 aataaatact ttaaggtaag gagactcgca tgaaacgttc tggcggcaca cgctatatgt
      181 atcttagcgc cctgataact gtggcagcag ccctcacggc ctgtacccca aaaaccagcc
      241 tggaacaaca tacccggcat tatgtttatg cttcagatga tgggtttgat cctaacttct
      301 acaccaagaa agctgacacc acacggatga tgattccgtt ctttcagcag ttccgggaga
      361 tgggggtgaa agacaaagca gctggagtat cagcagaaac ggcacagcaa cgcataaaag
      421 aattccactc tgaagaattc cttcagtcac tgagaaccac aaccaccttt gcgggcagaa
      481 aatacacgaa cggtgatatg ccatcaccgg aaaaaatgaa gctgctggct gacacgattt
      541 ctgcggttta tcttgatggc tacgagggca ggcagtaaag ggagacattt accataatcc
      601 cttaattgta cgcaccatta aaacgcgttg agcgcgattc tgacgcaggc accgcaaaaa
      661 gaaatgctta cccccaggaa aaccggaaaa atgcgtcagg atcgttttca gggcgttgca
      721 tgactatgca cgaaactgaa tagcgatctg tttgggcgca tacggtgccc atgaggcaca
      781 ttttcggaca ttttcagttc gtgaatccct ggctcattgc tacatatccg ggcagacacc
      841 cctggcagcg cccccagggg tgtgatgtaa aaaaggcgac gcgcccctag gggcgcccct
      901 acattaatta actgtttttt ctacagatag tcagtactga ccctaagtag ggtcgtcata
      961 gcgtcgccat agggtcgtcg acgacgtgct tttgtataaa tctgaataag aaaatacatt
     1021 tttaaaacca taacaacatg atttaaaaag taaatcagca aaaagttggt tttgcgtggg
     1081 gtgtgggcat ttcaggcatg agaacagact cgcgtttttc tggaagaact gcggggattt
     1141 ttgattaaac aatactcacc gcagagcgag attttatgca acagcggctg tactgcacag
     1201 gaattattta tcagttgata tgccgtgcca tgatattgct attgccgaaa gggacgtcgt
     1261 tttacggcat tttccctatc ctgcatcgca ctggccgcgt tcgaatgttt gcgcccctga
     1321 ctaaccgctc actcagcttt atcactctcg cctgcgtcac agttatcatg ctcccatgaa
     1381 cagaaattcc cttacacgga gacatcagac cagtgaccaa acaggaaaaa accgctctga
     1441 acatggcgcg cttcatcaga agccagacat taacgctgct ggagaagctc aacgaactgg
     1501 acgcagatga acaggcagat atctgtgaat cgcttcacga ccacgccgat gagctttacc
     1561 gcagttgcct cgcacgtttc ggggatgacg gtgaagccct ctgacacatg cagctcccgg
     1621 agacggtcac agcttgcctg tgagcggata ccgggagcag acaagcccgt caacgggttt
     1681 tagcgggtgt cggggcgcag ccatgaccca gtcacgtagc gatagcggag tgtatacggg
     1741 cttaaccatg cggcatgtcc agtgtgaaat gccgcacaga tgcgtaagga gaaaatgcca
     1801 gttcaggcgc tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg
     1861 gcgagcggag tccactcact caaaagctgt aatacaatta tccacagaat caggggataa
     1921 cgccggaaag aacatgtgag caaaagacca agaaccggaa gaaagccgca ccactggcgt
     1981 ttttccatag gctccgcccc cctgacgagc atcacaaaaa ttgacgctca agtcagaggt
     2041 ggcgaacccc gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc
     2101 gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa
     2161 gcgtggcgct ttctcatagc tcacgctgtt ggtatctcgg ctcggtgtag gtcgttcgct
     2221 ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta
     2281 actatcgtct tgagtccaac ccggtaagac acgacttaac gccactggca gcagccactg
     2341 gtaaccggat tagcagagcg atgatggcac aaatggtgct acagagttct tgaagttgtg
     2401 gcccgactgc ggctacactg gaaggacagt atttggtatc tgcgctctgc tgaagccagt
     2461 taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg ttggtagcgg
     2521 tggttttttt gtttgcaagc agcagattac gcgcagaaga aaaggatcac aagaggatca
     2581 gtgatgcaaa ctcacgattt cttcacttgg ataccgacac ctgagttaga tgacgaaaat
     2641 gaaccacctg aattaccttt aatattattc atctgacatg caaccaaaca aaatgatatg
     2701 attacaacac ctacaaaaaa cattttcttc atgtatactc ctttatataa aaacaagata
     2761 gtgagacatt aacatatgaa caagaaattc tatttctctc gtttattatg gggtctattt
     2821 cctatactta tcgcaatata taacttattc cacgaaccat tgacatcaaa aacaatacaa
     2881 atatcaatca tatatatact cagcggaata cttcttcctg tatctatgta cactgtaaaa
     2941 acagtagcat taagatatac atcaatacag ttttggaacc ccacttggtt aaactccaat
     3001 ggggttaatc gattttacgt tatatatgtg tttttttgtg ttattttcgc aatcccattc
     3061 agcattattt atctttttat agataaggac aagctggtca aaaaaaatga ccagcttaac
     3121 aaccattaaa tacctagttg cgagttaatt tcattaacta actgctcatc aaaaaaagag
     3181 cctgctaaag ccacaaggac accaaaacca acaatcccca taggaactcc tgtaataata
     3241 gaaaaaacaa ttgcagaaat agccacggct gcacgatttg cggtaataat ttctagttta
     3301 acaagaacag gtcgccaatt atctgttgtc aatgcatttt taagttcaac aagaatatca
     3361 gccagatcaa tagcatttcc taaataacca aatgctttac tatatttagc taaactgttt
     3421 gctgtattcg tagcatctaa tgcctgaatt cctgcgacaa tagcggcacg atcagcagaa
     3481 ttaaacttat cacccaaaga acttctatac cgatcaaatg cagccaaagc atcatcaaca
     3541 ccacgaatag tttttccatt agctttatca gccaaacttt tcgctaataa ttcagctttc
     3601 tcaccatact tttctgttac tttttcatag aaagtagctg tataggcaac agcatccttt
     3661 attttatcca catcgctttt caatgtgttt ttgtaatcat ataacttgct aatatcagca
     3721 tccaactgat tagattttct ttgtaactca tcaacatccc tttcaagatc agtaattcca
     3781 tgataggagt gatgcttgaa tatttttttc atctcctcta tttttttatt tttttcacta
     3841 atctgcgcag caatctgatt tttctggttc tgcttttcat caatcagagc actcaccatc
     3901 ttagaacttt tctccatatc actggctcga gtttctggag atactgcatt aacagcagtg
     3961 atgttattat cgtgattatt tcctgtcgcc ttggtaaaaa gtgatggcat atcactaatt
     4021 aaagagttaa gaactctgga gaccccccct aatggattat caaccaaaga agaattatct
     4081 tctgtcataa caacaccatt catcaccggg agaccatctt tattaataac aacatctccc
     4141 cacggggtta gatatgactc acctggcttc atcactgtcg atgttgaatt cgatgagctt
     4201 gtattaccct gaccaccatt attaccgtgt ccggagcctc ccccccagtg aacaccacta
     4261 ttattatgtc caccttgctg attcaaattc gcccctgttc cccccataga ttcaccggca
     4321 gttgggccat atccaccaag ttctttcgcc ataaaaaata cctctttgac attaaaaata
     4381 aatagttaaa accataatac tgtatatata accactggtt ttatatacag cttaaaatta
     4441 cgccgctgcg ttttccctgt caaccctgtg gattttcatt tttgtgaaaa cgttcaaaaa
     4501 aaaagccccc cacaccacga gctattcccg cccgatgcca caaaaaccag cacaaacatt
     4561 accgttctcc ggcctcagta tgttttactg aaaccatgat atgagacacc tatgggacac
     4621 tgtcacttta tggcatggca cacactccag gacgcactga aaatgacggg cagatcgcgt
     4681 tcacagtttt accgtgatat gcgcgcaggc cttgtcagtt accgtacaag ccaggacgga
     4741 cgacgggagt ttgaaaccag tgaactgatc cgggcatacg gcgaattaaa gcggaatgag
     4801 acaccagaaa ggcacactgc gggacaggca gaaaaacctc atgatcagca gacagaacgc
     4861 attctccggg agctgaacga gctgaaacaa tgcctgacgc tgatgcttga ggataaacaa
     4921 gctcaggata cggagcgcca gcgccaggaa gcagaacggg aacagctaca gaatgagata
//
