LOCUS       NZ_CP010161             3989 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli strain H1 plasmid A, complete sequence.
ACCESSION   NZ_CP010161
VERSION     NZ_CP010161.1
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 3989)
  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  JOURNAL   Unpublished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 3989)
  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
            CP010161.1.
            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..3989
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="H1"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="A"
                     /collection_date="2014"
     gene            join(3988..3989,1..190)
                     /locus_tag="RG44_RS25920"
                     /old_locus_tag="RG44_24045"
     CDS             join(3988..3989,1..190)
                     /locus_tag="RG44_RS25920"
                     /old_locus_tag="RG44_24045"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000166327.1"
                     /translation="MTKQQKTALNMAKFIQGQTLLLLEKLNELDLDVEADLCEKLHEDA
                     EQLCRTLTIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            190..621
                     /locus_tag="RG44_RS25925"
                     /old_locus_tag="RG44_24050"
     CDS             190..621
                     /locus_tag="RG44_RS25925"
                     /old_locus_tag="RG44_24050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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_073545078.1"
                     /translation="MARVSISEAARLASVSRPTIYKLLKSGELSYTSVVKHGKSVKAID
                     TTELIRVFGSLSFDSERDNAVVKFDEHSTGVNSNFLQDLQHQVALLQAENAGLKDAVNA
                     RNEHINSLRQAMQLLEHKQDTADPQHVPAKSWWQFWKSR"
                     /name="helix-turn-helix domain-containing protein"
     gene            1130..1351
                     /locus_tag="RG44_RS25930"
                     /old_locus_tag="RG44_24055"
     CDS             1130..1351
                     /locus_tag="RG44_RS25930"
                     /old_locus_tag="RG44_24055"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_073545079.1"
                     /translation="MKKWLATLIDDLKFLGAEFKREFSDLGITPVMAEQHQQRIAEMRR
                     STVAGKLSRGVLQIRDGVLTFYGMKTKW"
                     /name="hypothetical protein"
     gene            1917..2435
                     /locus_tag="RG44_RS25935"
                     /old_locus_tag="RG44_24060"
     CDS             1917..2435
                     /locus_tag="RG44_RS25935"
                     /old_locus_tag="RG44_24060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032436807.1"
                     /translation="MSERAKRSGRRSLSKRREELLEELWGEELDDLNIWNRAEHKGFTT
                     VPRTLNYINRIIDHLAGTGSPVSQTYLSLWCRVFDEGFVEIRDKDSIAYESGFNGQRAV
                     TTWMSRMKKLRELGLIKTKAGTSGEFHYVLMLNPLSIIKSHYESNGMSKDERYNALFSR
                     MQEVGAKWE"
                     /name="hypothetical protein"
     gene            2432..2992
                     /locus_tag="RG44_RS25940"
                     /old_locus_tag="RG44_24065"
     CDS             2432..2992
                     /locus_tag="RG44_RS25940"
                     /old_locus_tag="RG44_24065"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_073545080.1"
                     /translation="MSTFCGVRERYLKIYQEAFDEVVATYVEAGVLAGIELRLSPIDKT
                     ALSAWSSEWMGKSAKQKHGEWQWDRMVAKRIKRCKKFDLAIWGDGILCGLSLGLVTRGK
                     KTVRMNYLQACPVKHPLEKQIAAIAVAVAIAVGQRVGADHVAIFNPVNEKVENHYRKLG
                     FEKRTVYSRFVKNAMYMDIPSRD"
                     /name="hypothetical protein"
     gene            complement(2989..3156)
                     /locus_tag="RG44_RS27150"
     CDS             complement(2989..3156)
                     /locus_tag="RG44_RS27150"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_159427097.1"
                     /translation="MSYVADTKARNEEAKLVREETSSNSRKPSNKGLLAFIVASAAVDD
                     FEQRGRIHGA"
                     /name="hypothetical protein"
     gene            complement(3459..3572)
                     /locus_tag="RG44_RS26540"
     CDS             complement(3459..3572)
                     /locus_tag="RG44_RS26540"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_077897077.1"
                     /translation="MHEPPVQSDCYALSGNYQLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(3456..3809)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.493"
                     /coverage="82.0"
                     /evalue="2.95e-159"
ORIGIN
        1 gacgaaacaa cagaaaactg cgcttaatat ggcgaagttt atccaggggc agaccctgct
       61 tttgttggaa aagcttaatg aactcgatct cgatgttgag gcggatcttt gtgaaaagct
      121 ccatgaggat gcggaacaac tctgtcgtac tctgactatt cgtctggatg gtcatcaggg
      181 ggatttataa tggccagggt atctattagc gaagcggcac gccttgccag tgtcagtcgt
      241 ccgactattt acaagttact caaatctggt gagttaagtt acacctctgt tgtaaagcat
      301 ggaaaatctg taaaagcaat tgatactaca gagcttattc gtgttttcgg ctctcttagt
      361 tttgacagtg aacgtgacaa tgccgttgta aaatttgacg aacactctac aggtgttaac
      421 agtaattttt tacaggattt acagcatcag gtggcacttt tgcaggcaga aaacgccggg
      481 ctgaaagatg cagtgaatgc ccggaatgaa catatcaact cacttcgcca ggctatgcag
      541 ctgctggagc ataaacagga cactgctgat ccgcagcatg tccctgcaaa gtcctggtgg
      601 cagttctgga aatcccgctg agtcattacc acgcattccg gccatagcgt tcgtcctgcc
      661 actcagtttc tgccggatat ggatttttgt actcttttgt cctgctgatt ttcctgcatg
      721 tttgactcct gatggctgag aaaggccata aaatcgtgtc acaccccacg cattatgcaa
      781 tgcaaagccc aaagccgtgc tgagactggc tttggggggg catgacaccc aatgtgcaaa
      841 tgtcatgcat ttttttatga aattggactg aaagcccaga gttacaggcg ttcgcggcgt
      901 catgcccccc cctgcatgat gcttctctca ttttattcat ataatgtgtt gattttaatt
      961 attattttta cctgttcgac gtgcatgact tttcccgttg ctaaatttgc tagacgatcc
     1021 tgccagcgcc tcacgacccc gcaataaatt gcgtgcccgt tcaccgcttt ctttctccag
     1081 tctgtgccag actgttatct gaataactta aatgatgtga ggcagaacgg tgaaaaaatg
     1141 gcttgcgacc cttatcgatg acctgaagtt tctgggggct gagtttaaga gagagttttc
     1201 ggatctgggt atcacccctg tgatggccga gcaacatcag cagagaatag ctgaaatgcg
     1261 ccgttccacc gtagccggga agttatcccg gggtgttttg caaatcaggg acggggtact
     1321 gaccttttat ggcatgaaaa cgaaatggta ggcttccgcc cggaaatccg ggcaggaaaa
     1381 ccgggaaaaa tcgcggtttc accagctttt ttgtgccagg cctgagctca ttcactgcgc
     1441 tgcataatca ttcacaggcc gtaaacgcgc tcagatcgat tctggcgcgt ttttgccgga
     1501 taagctgtgg ttttcatcgt cttcgcgccg aaatcgcact cagcgcgttt tagcggtgcg
     1561 cgtaatgaga cgttatggta aatgcactca agtagcttta ctaacttagt tttatgccca
     1621 tccatactat ctgcccccct ttgcataccc ccttggagta ccgcgagcac aatgagaaca
     1681 atatgagaac aatcagaaca gcgagtacaa aatgtgttgt aacttactgt tttataaaac
     1741 gcttactgta atatatatta catctcaatt attgttttgt aatttattta atatcttgta
     1801 gtgtgtgctg tattgacctt tgactctttg tttttgaatg ttctcgtata actcattgaa
     1861 ataaaatgaa tttttataga gaatgagaga gttgactggc tgtaaggatg attgatatgt
     1921 cagaacgagc aaaaagatct ggacggcgct ctttgtcaaa gcgaagagaa gagcttcttg
     1981 aagaactatg gggtgaggaa cttgatgatt taaatatatg gaatagggct gagcataaag
     2041 gttttacgac cgttccaaga acattaaatt acatcaaccg tatcattgat cacttagctg
     2101 gtaccggctc cccagtgtct caaacgtact tgagcttatg gtgccgggtg tttgatgaag
     2161 gttttgttga aatcagagac aaagactcca tcgcttatga gtcagggttt aatgggcaga
     2221 gagctgtgac tacatggatg agtcggatga agaaactgcg tgagttaggg ctcatcaaga
     2281 caaaggccgg cacgtctggt gagtttcact atgtattaat gctgaatcca ctaagtatta
     2341 taaaaagtca ttatgaatca aatggtatga gtaaagatga gcggtataac gctctatttt
     2401 ctcgaatgca agaagtgggg gctaagtggg aatgagtaca ttttgtgggg ttcgtgagcg
     2461 ataccttaaa atttatcaag aagcatttga tgaggtcgtt gctacatacg ttgaagctgg
     2521 tgttttagct gggattgaac tgcgtttatc tccaatcgat aaaacggctt tatctgcatg
     2581 gtcttcggag tggatgggga aatcagctaa gcaaaaacat ggagaatggc agtgggatag
     2641 aatggtcgcc aagcggatta aacgatgtaa gaagtttgat ctggcaattt ggggtgatgg
     2701 gattctatgt ggactctctc ttggcctggt cacccgagga aagaaaactg tccgaatgaa
     2761 ttatttgcaa gcgtgtcctg taaagcaccc tttggaaaag caaatagccg ctattgcggt
     2821 tgcggttgcg attgctgtag gacagcgggt tggcgctgac catgtagcaa ttttcaaccc
     2881 tgtaaatgag aaggtcgaaa accactacag gaagttagga tttgaaaaaa ggacggtata
     2941 cagccggttt gtgaagaatg ctatgtatat ggacattcca agccgagatt aagcgccgtg
     3001 tatacggcct ctctgctcga aatcatcgac agctgcggaa gcaacaataa aggcaagcag
     3061 gcctttgttg gaaggtttgc ggctgtttga tgatgtttct tcgcgaacca atttagcctc
     3121 ttcatttctg gctttggtgt ctgctacgta actcatattt atagcctctg cttaacgtgt
     3181 agtatcacta tacaacatct ttgttttaaa aataactata agtagccaga taagcaacca
     3241 caacaagctg tgagtattgt tgactcctgg ctgttcatca gcgtaatctt ttgctctgta
     3301 aacgaaaaaa accacccggc aaggtggttt tttcgaaggt tcattaaccg gcaagtttct
     3361 gaaccgaggt aactggctaa tgaggagcgc agtaaccaaa acttgttctt tcagtttagc
     3421 cttaacaggc gcataacttc aagactaact cctctaaatc agttaccagt ggctgctgcc
     3481 agtggcgctt tgtcgtgtct ttccggcttg gactcaagtt gatagttacc ggataaggcg
     3541 tagcagtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc
     3601 ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc
     3661 ggtaaaccga aaggcaggaa caggagagcg cacgagggag ccgccagggg gaaacgcctg
     3721 gtatctttat agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga ttctgtgatg
     3781 cttatcaggg gggcgaagcc tatggaaaaa cgcccgtggg gcgtggcctt gtcgttctct
     3841 ttctggtttt tcgttacgct ttccgtctac gttatttgtc tcttcgaaag atccgtccgc
     3901 tcgccgcaga caagtgaccg agcgtagcga gcgaacggtc gaggaagcgg aaaagaaccg
     3961 gatatcactt ggagcactga cgctgtgat
//
