LOCUS       NZ_CP010182             4980 bp    DNA     circular CON 13-JUN-2024
DEFINITION  Escherichia coli strain M1 plasmid B, complete sequence.
ACCESSION   NZ_CP010182
VERSION     NZ_CP010182.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03252439
            Assembly: GCF_001901025.1
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  JOURNAL   Unpublished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 :: Illumina Miseq; Roche 454 GS Junior
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001901025.1-RS_2024_06_13
            Annotation Date                   :: 06/13/2024 02:47:11
            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)                     :: 5,034
            CDSs (total)                      :: 4,907
            Genes (coding)                    :: 4,707
            CDSs (with protein)               :: 4,707
            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)       :: 88 of 200
            Pseudo Genes (incomplete)         :: 120 of 200
            Pseudo Genes (internal stop)      :: 44 of 200
            Pseudo Genes (multiple problems)  :: 47 of 200
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP010182.1.
            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="M1"
                     /isolation_source="feces"
                     /host="mouse"
                     /db_xref="taxon:562"
                     /plasmid="B"
                     /collection_date="2014"
     gene            join(4918..4980,1..129)
                     /locus_tag="RG54_RS27130"
                     /old_locus_tag="RG54_25585"
     CDS             join(4918..4980,1..129)
                     /locus_tag="RG54_RS27130"
                     /old_locus_tag="RG54_25585"
                     /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(1117..1257)
                     /locus_tag="RG54_RS28475"
     CDS             complement(1117..1257)
                     /locus_tag="RG54_RS28475"
                     /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(1651..2877)
                     /locus_tag="RG54_RS27155"
     CDS             complement(1651..2877)
                     /locus_tag="RG54_RS27155"
                     /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"
     gene            3137..3574
                     /locus_tag="RG54_RS27160"
                     /old_locus_tag="RG54_25600"
     CDS             3137..3574
                     /locus_tag="RG54_RS27160"
                     /old_locus_tag="RG54_25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /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_170981958.1"
                     /translation="MGHCHFMAWHTLQDALKMTGRSRSQFYRDMRAGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTAGQAEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERQRQEAEREQLQNEIAQLRQALEQEKKRGVWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            3655..4083
                     /locus_tag="RG54_RS27165"
                     /old_locus_tag="RG54_25605"
     CDS             3655..4083
                     /locus_tag="RG54_RS27165"
                     /old_locus_tag="RG54_25605"
                     /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"
     Typing          288..832
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.698"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctgctggaga agctcaacga actggacgca gatgaacagg cagatatctg tgaatcgctt
       61 cacgaccacg ccgatgagct ttaccgcagt tgcctcgcac gtttcgggga tgacggtgaa
      121 gccctctgac acatgcagct cccggagacg gtcacagctt gcctgtgagc ggataccggg
      181 agcagacaag cccgtcaacg ggttttagcg ggtgtcgggg cgcagccatg acccagtcac
      241 gtagcgatag cggagtgtat acgggcttaa ccatgcggca tgtccagtgt gaaatgccgc
      301 acagatgcgt aaggagaaaa tgccagttca ggcgctcttc cgcttcctcg ctcactgact
      361 cgctgcgctc ggtcgttcgg ctgcggcgag cggagtccac tcactcaaaa gctgtaatac
      421 aattatccac agaatcaggg gataacgccg gaaagaacat gtgagcaaaa gaccaagaac
      481 cggaagaaag ccgcaccact ggcgtttttc cataggctcc gcccccctga cgagcatcac
      541 aaaaattgac gctcaagtca gaggtggcga accccgacag gactataaag ataccaggcg
      601 tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac
      661 ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgttggtat
      721 ctcggctcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag
      781 cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt aagacacgac
      841 ttaacgccac tggcagcagc cactggtaac cggattagca gagcgatgat ggcacaaatg
      901 gtgctacaga gttcttgaag ttgtggcccg actgcggcta cactggaagg acagtatttg
      961 gtatctgcgc tctgctgaag ccagttacct tcggaaaaag agttggtagc tcttgatccg
     1021 gcaaacaaac caccgttggt agcggtggtt tttttgtttg caagcagcag attacgcgca
     1081 gaagaaaagg atcacaagag gatcagtgat gcaaactcac gatttcttca cttggatacc
     1141 gacacctgag ttagatgacg aaaatgaacc acctgaatta cctttaatat tattcatctg
     1201 acatgcaacc aaacaaaatg atatgattac aacacctaca aaaaacattt tcttcatgta
     1261 tactccttta tataaaaaca agatagtgag acattaacat atgaacaaga aattctattt
     1321 ctctcgttta ttatggggtc tatttcctat acttatcgca atatataact tattccacga
     1381 accattgaca tcaaaaacaa tacaaatatc aatcatatat atactcagcg gaatacttct
     1441 tcctgtatct atgtacactg taaaaacagt agcattaaga tatacatcaa tacagttttg
     1501 gaaccccact tggttaaact ccaatggggt taatcgattt tacgttatat atgtgttttt
     1561 ttgtgttatt ttcgcaatcc cattcagcat tatttatctt tttatagata aggacaagct
     1621 ggtcaaaaaa aatgaccagc ttaacaacca ttaaatacct agttgcgagt taatttcatt
     1681 aactaactgc tcatcaaaaa aagagcctgc taaagccaca aggacaccaa aaccaacaat
     1741 ccccatagga actcctgtaa taatagaaaa aacaattgca gaaatagcca cggctgcacg
     1801 atttgcggta ataatttcta gtttaacaag aacaggtcgc caattatctg ttgtcaatgc
     1861 atttttaagt tcaacaagaa tatcagccag atcaatagca tttcctaaat aaccaaatgc
     1921 tttactatat ttagctaaac tgtttgctgt attcgtagca tctaatgcct gaattcctgc
     1981 gacaatagcg gcacgatcag cagaattaaa cttatcaccc aaagaacttc tataccgatc
     2041 aaatgcagcc aaagcatcat caacaccacg aatagttttt ccattagctt tatcagccaa
     2101 acttttcgct aataattcag ctttctcacc atacttttct gttacttttt catagaaagt
     2161 agctgtatag gcaacagcat cctttatttt atccacatcg cttttcaatg tgtttttgta
     2221 atcatataac ttgctaatat cagcatccaa ctgattagat tttctttgta actcatcaac
     2281 atccctttca agatcagtaa ttccatgata ggagtgatgc ttgaatattt ttttcatctc
     2341 ctctattttt ttattttttt cactaatctg cgcagcaatc tgatttttct ggttctgctt
     2401 ttcatcaatc agagcactca ccatcttaga acttttctcc atatcactgg ctcgagtttc
     2461 tggagatact gcattaacag cagtgatgtt attatcgtga ttatttcctg tcgccttggt
     2521 aaaaagtgat ggcatatcac taattaaaga gttaagaact ctggagaccc cccctaatgg
     2581 attatcaacc aaagaagaat tatcttctgt cataacaaca ccattcatca ccgggagacc
     2641 atctttatta ataacaacat ctccccacgg ggttagatat gactcacctg gcttcatcac
     2701 tgtcgatgtt gaattcgatg agcttgtatt accctgacca ccattattac cgtgtccgga
     2761 gcctcccccc cagtgaacac cactattatt atgtccacct tgctgattca aattcgcccc
     2821 tgttcccccc atagattcac cggcagttgg gccatatcca ccaagttctt tcgccataaa
     2881 aaatacctct ttgacattaa aaataaatag ttaaaaccat aatactgtat atataaccac
     2941 tggttttata tacagcttaa aattacgccg ctgcgttttc cctgtcaacc ctgtggattt
     3001 tcatttttgt gaaaacgttc aaaaaaaaag ccccccacac cacgagctat tcccgcccga
     3061 tgccacaaaa accagcacaa acattaccgt tctccggcct cagtatgttt tactgaaacc
     3121 atgatatgag acacctatgg gacactgtca ctttatggca tggcacacac tccaggacgc
     3181 actgaaaatg acgggcagat cgcgttcaca gttttaccgt gatatgcgcg caggccttgt
     3241 cagttaccgt acaagccagg acggacgacg ggagtttgaa accagtgaac tgatccgggc
     3301 atacggcgaa ttaaagcgga atgagacacc agaaaggcac actgcgggac aggcagaaaa
     3361 acctcatgat cagcagacag aacgcattct ccgggagctg aacgagctga aacaatgcct
     3421 gacgctgatg cttgaggata aacaagctca ggatacggag cgccagcgcc aggaagcaga
     3481 acgggaacag ctacagaatg agatagccca gctcaggcag gcgctggagc aggaaaagaa
     3541 acggggagtc tggtccaggt tgttcggtcg ctgaacgcac tcagagactg atgataagat
     3601 agccatcaga taataactca ccgaaaataa atactttaag gtaaggagac tcgcatgaaa
     3661 cgttctggcg gcacacgcta tatgtatctt agcgccctga taactgtggc agcagccctc
     3721 acggcctgta ccccaaaaac cagcctggaa caacataccc ggcattatgt ttatgcttca
     3781 gatgatgggt ttgatcctaa cttctacacc aagaaagctg acaccacacg gatgatgatt
     3841 ccgttctttc agcagttccg ggagatgggg gtgaaagaca aagcagctgg agtatcagca
     3901 gaaacggcac agcaacgcat aaaagaattc cactctgaag aattccttca gtcactgaga
     3961 accacaacca cctttgcggg cagaaaatac acgaacggtg atatgccatc accggaaaaa
     4021 atgaagctgc tggctgacac gatttctgcg gtttatcttg atggctacga gggcaggcag
     4081 taaagggaga catttaccat aatcccttaa ttgtacgcac cattaaaacg cgttgagcgc
     4141 gattctgacg caggcaccgc aaaaagaaat gcttaccccc aggaaaaccg gaaaaatgcg
     4201 tcaggatcgt tttcagggcg ttgcatgact atgcacgaaa ctgaatagcg atctgtttgg
     4261 gcgcatacgg tgcccatgag gcacattttc ggacattttc agttcgtgaa tccctggctc
     4321 attgctacat atccgggcag acacccctgg cagcgccccc aggggtgtga tgtaaaaaag
     4381 gcgacgcgcc cctaggggcg cccctacatt aattaactgt tttttctaca gatagtcagt
     4441 actgacccta agtagggtcg tcatagcgtc gccatagggt cgtcgacgac gtgcttttgt
     4501 ataaatctga ataagaaaat acatttttaa aaccataaca acatgattta aaaagtaaat
     4561 cagcaaaaag ttggttttgc gtggggtgtg ggcatttcag gcatgagaac agactcgcgt
     4621 ttttctggaa gaactgcggg gatttttgat taaacaatac tcaccgcaga gcgagatttt
     4681 atgcaacagc ggctgtactg cacaggaatt atttatcagt tgatatgccg tgccatgata
     4741 ttgctattgc cgaaagggac gtcgttttac ggcattttcc ctatcctgca tcgcactggc
     4801 cgcgttcgaa tgtttgcgcc cctgactaac cgctcactca gctttatcac tctcgcctgc
     4861 gtcacagtta tcatgctccc atgaacagaa attcccttac acggagacat cagaccagtg
     4921 accaaacagg aaaaaaccgc tctgaacatg gcgcgcttca tcagaagcca gacattaacg
//
