LOCUS       NZ_CP029114             3656 bp    DNA     linear   CON 16-JUN-2024
DEFINITION  Escherichia coli strain AR435 plasmid unnamed2.
ACCESSION   NZ_CP029114
VERSION     NZ_CP029114.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07291528
            Assembly: GCF_003073835.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3656)
  AUTHORS   Benahmed,F.H., Lutgring,J.D., Yoo,B., Machado,M., Brown,A.,
            McAllister,G., Perry,A., Halpin,A.L., Vavikolanu,K., Ott,S.,
            Zhao,X., Tallon,L.J., Sadzewicz,L., Aluvathingal,J., Nadendla,S.,
            Voskania-kordi,A., Simonyan,V., Patel,J. and Shawar,R.M.
  TITLE     FDA/CDC Antimicrobial Resistant Isolate Bank Genome Sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3656)
  AUTHORS   Benahmed,F.H., Lutgring,J.D., Yoo,B., Machado,M., Brown,A.,
            McAllister,G., Perry,A., Halpin,A.L., Vavikolanu,K., Ott,S.,
            Zhao,X., Tallon,L.J., Sadzewicz,L., Aluvathingal,J., Nadendla,S.,
            Voskania-kordi,A., Simonyan,V., Patel,J. and Shawar,R.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-APR-2018) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Sring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 2.3.0; HGAP v. 3.0; SPAdes v. 3.6.0
            Genome Coverage                   :: 14.36x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003073835.1-RS_2024_06_15
            Annotation Date                   :: 06/15/2024 04:07:09
            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)                     :: 5,275
            CDSs (total)                      :: 5,152
            Genes (coding)                    :: 4,858
            CDSs (with protein)               :: 4,858
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 294
            CDSs (without protein)            :: 294
            Pseudo Genes (ambiguous residues) :: 0 of 294
            Pseudo Genes (frameshifted)       :: 107 of 294
            Pseudo Genes (incomplete)         :: 192 of 294
            Pseudo Genes (internal stop)      :: 63 of 294
            Pseudo Genes (multiple problems)  :: 61 of 294
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP029114.1.
            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/
FEATURES             Location/Qualifiers
     source          1..3656
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AR435"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
     gene            <1..181
                     /locus_tag="CSC22_RS28515"
     CDS             <1..181
                     /locus_tag="CSC22_RS28515"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=2
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_204100969.1"
                     /translation="FPSENGERGRNLLRGREALPAQPENRFSARSGIVFVDGRQSRHGK
                     SPDDSPHDSPATLH"
                     /name="hypothetical protein"
     gene            complement(534..956)
                     /locus_tag="CSC22_RS00780"
     CDS             complement(534..956)
                     /locus_tag="CSC22_RS00780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_039023181.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVLKHGKTIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(956..1147)
                     /locus_tag="CSC22_RS00785"
                     /old_locus_tag="CSC22_0010"
     CDS             complement(956..1147)
                     /locus_tag="CSC22_RS00785"
                     /old_locus_tag="CSC22_0010"
                     /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_039023180.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1552..1698
                     /locus_tag="CSC22_RS28900"
     CDS             1552..1698
                     /locus_tag="CSC22_RS28900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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_073545459.1"
                     /translation="MHEPPVQSDCCTLSGNYHLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            complement(2156..2437)
                     /locus_tag="CSC22_RS00795"
     CDS             complement(2156..2437)
                     /locus_tag="CSC22_RS00795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2774..3067
                     /locus_tag="CSC22_RS00800"
     CDS             2774..3067
                     /locus_tag="CSC22_RS00800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            3131..3433
                     /locus_tag="CSC22_RS00805"
                     /old_locus_tag="CSC22_0011"
     CDS             3131..3433
                     /locus_tag="CSC22_RS00805"
                     /old_locus_tag="CSC22_0011"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_039023182.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMDDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     Typing          1289..1661
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 cttcccatcc gaaaacggtg aacggggacg caatttattg cgtggccgtg aagcgttgcc
       61 ggcgcagccg gaaaaccggt tttcagcacg ttcaggaatc gtgttcgtcg acggccggca
      121 atcacgtcat ggcaagtcgc cggacgactc accacacgat tcaccggcga ctcttcacta
      181 gagtcgtacc cagagtcgcc gagtctaaaa aacaaccaaa cggggagtcg ggtctagagt
      241 cgggtcgtta ttaactcatt gtttttatag ctctgagtcg ttaccgactc tatgacgact
      301 cgccggggac tctatgacga gtcgtcatag agtcggatct atgtaaataa aatttaaaaa
      361 ccgaaacttc aggaaagtaa gctactgata ttaaatacaa atctgcaaaa ttttaatttt
      421 gcgtagtgtg tgggtatttt tagtcgtgag gagcgttcag agatctggcg atttttggga
      481 aggttcagga actccccggg atggccggag aggaaaacgg aagcatgacg gagtcaggat
      541 tttttccaga atttccacca cggggaatcg ggtggtgaag aaggttcgtg cttgtgctcc
      601 agaagctgca tagcctgacg aagggaatca atatgctcat ctcgagcctt aacagcccct
      661 ttaagaccat cgttttcagc ttctagtaaa gcaattctat gttgtaaatc atgtaaacca
      721 acgctgttaa cacctgtaga tcctgcgtca ctttttacat catattttac agtatcgatg
      781 acaccatcaa gagaaccaaa aactctaata agctctgaag tatcaataac tttaatggtc
      841 ttcccgtgct ttaaaacaga ggtgtaactt aacttcccac tgttaatcat cttgtaaatt
      901 gtggggcgac taaccttaac aagccgtgcc gcttcactaa tagacactct ggccatcagt
      961 taccatcctg taattcatcc agtctcgagg acagtgtacg gaaaagatgc tccgcatcat
     1021 cgtggagttt ctcacaaagg tcggcctctg catcaagatc aagctcgtta agcttctcca
     1081 gcaggagcag agactgattc tggatgaatt tagccatgtt cagcgctgtt ttctgttgtt
     1141 tcgacataag aggcctcaga gcgtcagtgc tcagtgtagg tatgttctct tttccgcttc
     1201 ctcgctcact cagtcgctac gctcctgccg ttcggctgcg gcgagcggtc gcaatacaca
     1261 cataacgaca taggacagac agcacggaga gggagaaggc cgcacaccgg ccgtttttcc
     1321 ataggctccg cccccctgac aagcatcacg aaatctgacg ctcaaatcag tggtggcgaa
     1381 ccccgacagg actataaaga taccaggcgt ttccccctga tggctccctc gtgcgctctc
     1441 ctgttcctgc ctttcggttt accggtgtca ttccgctgtt atggccgcgt ttatctcatt
     1501 ccacgccaga cactcagttc cgggtaggca gttcgctcca agctggactg tatgcacgaa
     1561 ccccccgttc agtccgactg ctgcacctta tccggtaact atcatcttga gtccaacccg
     1621 gtaagacacg cacaagcgcc actggcagca gccactggta agaaggtgta caagagatta
     1681 ctgatacaga gttcttgaag tctcagccca actacggcta aactgaaagg acagaatttg
     1741 gtttcagcgg tcttgtacac cctgttacca cggttcagaa gttccccaac ttactgaacc
     1801 ctcgaaaaaa ccgcctcccc aggcggtttt ttcgtctcgg cgagtaagat acgctttatc
     1861 attcaaagca gtcaaggaag aaccaagaca gctcactcac cagcaggctc ctttttattg
     1921 gtagacacat gcttctggac agtatcagcc cctgcacaaa gtacagcagc taacaagaac
     1981 catccccagc catcaatacc acgaaaagct aggactccag caatagttac gctaatcaac
     2041 gggaacaata aaaccataaa ggatctcata ctttctccag aggttacttt tttaataaag
     2101 tccctaatcc atccgtactt tcacttggat ggattagcaa cttacttatt gataactaat
     2161 gataatcttc aagatcaacg tctaagacgt ttggttcctc aaccttgaaa actacccgcc
     2221 agttcccatt aacttcaacg gaatactcgc ctttacgctc cccctttagg gggtggcacc
     2281 ctaacgccct aacgtcaaca acgtcttgaa tgcaagttgc tgtgcttagc gtagtcaaaa
     2341 tcatgcgaag tcttttcgcc atactgggct gaataccggc ggtgctacct tcttcagcaa
     2401 agctcctaag tcctttatgt tttatgtttt ttatcatcta caatccccat atttttttcg
     2461 tctatacctg tatctatatt ttaaaatcat tttaattagt tccattttgc ccccttgctt
     2521 tattaaaaca attgacgtaa gtttgttctt gaggtcaatc acctcatttg acttcaacga
     2581 atcctaaggg taaaatactg cgccttgaaa aggccataaa agcccataca tacgcagtag
     2641 ctttgactcc aacgagtatc ctaaagctga ctgctttttt tgtcaatatc atgaacttgc
     2701 acattgtgca atgcgcatac tgaaaggcag taattttttt gtataatcaa atacaaaaca
     2761 aacagaggaa ggcatgataa atctttacga tcctgttcat cctggtgagt ttatcagaga
     2821 aatgttcatg gaaccgttcg aaatacctgc cgcagagtta gccgataaac ttgatgtatc
     2881 ccagtctacc ttaagtagac tgttaaatgg gaaaacagac ttaagctatg aaatggcact
     2941 tagattgtcg aaggtcgtag gccgctctgc agagtcgtgg gtaaacatgc agacccaatt
     3001 cagcctgtca aaaagtcgca aatctttagc ggcagagctg gaacacttgc atccaatgtt
     3061 tccatgaaaa aagcccgcag aacgcgggct tttgttacgt aaaacaccca gcagccatca
     3121 ggaggcaacc atggtagatt tctatatctc agcaatcaaa atggacagtg ctggtcagca
     3181 catcgaattc gtaaaagttc ataaaataaa ccgagatggc tcatggaaca ctgccggctc
     3241 aatcagctct cgcaaattca tcagcgagct gatcagcatg ggaaaagcca gctttatgac
     3301 agttgtaaag aacagctcta ctggtaagtg gaacctagga gccaaagtgg aagcgatgga
     3361 cgatggctac ataaccacag atccaaacaa aactaaactc gataacttgg gaaatctgcc
     3421 gaaatttgtc tgatatgcaa taacatccac taagttccag cagaatcccc tccctaatga
     3481 tttaacataa agtcataatt gtacgcaccg ccagaacggc ctcagggcgt ttctgacagg
     3541 aaaccggtaa aacaggcaac aaaccacccg aaaacccgtc agaaacgcgc aggctctgtt
     3601 tttacggcat gcatgagtat gcacgcaagt gcatagcgcg aaaattcacg ccattc
//
