LOCUS       NZ_CP069896             5014 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1286 plasmid unnamed3.
ACCESSION   NZ_CP069896
VERSION     NZ_CP069896.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357428
            Assembly: GCF_016903375.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5014)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5014)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-FEB-2021) Institute for Genome Sciences, University of
            Maryland School of Medicine, BioPark II, 801 W. Baltimore St., Suite
            619, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 8.0.0, HGAP v. 4
            Genome Coverage                   :: 1520.67x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:01:12
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,075
            CDSs (total)                      :: 4,949
            Genes (coding)                    :: 4,749
            CDSs (with protein)               :: 4,749
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 79 of 200
            Pseudo Genes (incomplete)         :: 130 of 200
            Pseudo Genes (internal stop)      :: 52 of 200
            Pseudo Genes (multiple problems)  :: 57 of 200
            Pseudo Genes (short protein)      :: 5 of 200
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069896.1.
            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..5014
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1286"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1286"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            <1..135
                     /locus_tag="I6K16_RS24965"
                     /old_locus_tag="I6K16_24965"
                     /pseudo=""
     CDS             <1..135
                     /locus_tag="I6K16_RS24965"
                     /old_locus_tag="I6K16_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /name="nikA protein"
     gene            complement(360..779)
                     /locus_tag="I6K16_RS24970"
                     /old_locus_tag="I6K16_24970"
     CDS             complement(360..779)
                     /locus_tag="I6K16_RS24970"
                     /old_locus_tag="I6K16_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /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_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(860..1297)
                     /locus_tag="I6K16_RS24975"
                     /old_locus_tag="I6K16_24975"
     CDS             complement(860..1297)
                     /locus_tag="I6K16_RS24975"
                     /old_locus_tag="I6K16_24975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001318234.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            1557..3122
                     /locus_tag="I6K16_RS24980"
                     /old_locus_tag="I6K16_24980"
     CDS             1557..3122
                     /locus_tag="I6K16_RS24980"
                     /old_locus_tag="I6K16_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [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_000447003.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(3119..3460)
                     /locus_tag="I6K16_RS24985"
                     /old_locus_tag="I6K16_24985"
     CDS             complement(3119..3460)
                     /locus_tag="I6K16_RS24985"
                     /old_locus_tag="I6K16_24985"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 family microcin immunity protein"
     gene            3508..3645
                     /locus_tag="I6K16_RS24990"
                     /old_locus_tag="I6K16_24990"
     CDS             3508..3645
                     /locus_tag="I6K16_RS24990"
                     /old_locus_tag="I6K16_24990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /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: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(4487..4681)
                     /locus_tag="I6K16_RS24995"
                     /old_locus_tag="I6K16_24995"
     CDS             complement(4487..4681)
                     /locus_tag="I6K16_RS24995"
                     /old_locus_tag="I6K16_24995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4717..4956
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(3929..4458)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.59"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 gttatgagac tgggggcgtt acagaaaaaa ctctttatcg acggcaagcg tgtcggggac
       61 agggagtatg cggaggtgct gatcgctatt acggagtatc accgtgccct gttatccagg
      121 cttatggcag attagcttcc cggagagaaa actgtcgaaa actgacggta tgaacaccgt
      181 aagctcccaa agtgatcacc attcgctttc atgcatagct atgcagagag ctgaaaacga
      241 tcctgacgca tccttcctgt ttttccgggg taaaacatct ctttttgcgg tgtctgcgtc
      301 agaatcgcgt tcagcgcgtt tcagtggtgc gtacaattaa gggattatgg taaatccact
      361 tactgtctgc cctcgtagcc atcgagataa accgcagaaa tcgtgtcagc cagcagcctg
      421 gattttttcg gggtaaggtc tttgctgcgg taatcagtac ccgcaaattg agttgtgccc
      481 cggagtgagt ttaaaaattc ctggctgtga aactgttgaa tgcgttgttg cacatcactc
      541 cgtgattttc ctgtcgcttt atctttagct cccatatccc agaactgccg aaaaaaaggc
      601 accatcattc gtgttgtgtc ggctttttgg gtggaaaagt tgggatcaaa accgtcatca
      661 gaagcatata cgtaatgccg ggtatgttgt tccacgctgc cctttggggt acaggctgtg
      721 agagctactg ttgctgttat catggcgata agacaaagtt tgtttccggt acgtctcatg
      781 agtgtctccc taccttaaag tatttattct cggtgagtta ttatccgaag attatcttat
      841 catcagtttc tgagcgcgtt cagtgaccga acagcctgga ccagaatccc cgtttctttt
      901 cctgctccag agcctgcctg agctgggcta tctcattctg tagctgtttc cgttctgctt
      961 cctggcgccg gcgctccgta tcctgggctt gtttatcctc aagcatcagc gtcaggcatt
     1021 gtttcagctc attcagttcc cggagaatgc gttctgtctg ctgatcatga ggtttttctg
     1081 agtgtccttg agtgtgcctt tctggtgtct cattccgctt taattcgccg tatgcccgga
     1141 tcagttcact ggtttcaaac tcccgtcgtc cgtcctggct ggtacggtaa ctgacaagac
     1201 ctgagcgcat atcacggtaa aactgtgaac gcgatcttcc agtcattttc agtgcgtccc
     1261 ggagtgtgtg ccatgccata aagttacagt gtcccatagg tgtctcatct catggtttca
     1321 gtaaaacata atgaggtctg agaacggtaa tgtttgtgct ggtttttgtg gcatcgggtg
     1381 gaaatagcac gtggtgtggg tggctgtttt tttgatcgtt ttcacaaaaa tgaaaatcca
     1441 cagggttgac agggaaaatg cagcggcgta attttaaact gtatataaaa ccagtgatta
     1501 tatatacagt atattgcttt taactatttg tttttaatgt caaagaggat tttataatgg
     1561 aaacagctgt agcgtactat aaagatggtg ttccttatga tgataagggg caggtaatca
     1621 ttactctttt gaatggtaat ccagacggga gtggctctgg cggtggtggt ggaactggag
     1681 gtagcaaaag tgaaagttct gcagccattc atgccacagc taaatggtct actgctcaat
     1741 tgaagaaaac gcaggcagaa caggctgccc gagcaaaagc tgccgcagaa gcacaggcta
     1801 aagcaaaagc aaaccgggat gcgctgactc aacatctgaa ggatattgtg aatgaggcgc
     1861 ttcgccataa ttccactcat ccggaggtta ttgacctggc tcatgccaat aatgcagcga
     1921 tgcaggcaga agcagagcgg ttgcgccttg caaaagcaga agaaaaagcc cgtaaagaag
     1981 cggaagctgc ggaaaaggct tttcaggaag cagaacaacg acgtaaagag atagagaagg
     2041 agcaggctga aacagaacgc caattgaaac tggctgagga tgaagagaaa cgcctggcag
     2101 cattgagtga agaggcccgg gctgtggagg tggcacaaaa aaatcttgct gctgcacaat
     2161 ctgagctggc gaaagtggat gaagagatta atacgctcaa tacccgttta agctccagta
     2221 ttcatgcccg tgatgcagaa acgaatacgc tgtccggaaa acgaaatgag ttggatcagg
     2281 catctgctaa atataaagaa ctggatgaaa gggttaaact tttatctcct agggcgaatg
     2341 atccgcttca gagtcgtcct ttttttgagg ccaccagact acgggcgaga gctggtgatg
     2401 agatggagga aaaacaaaag caggtaacag catcagaaac gcgtcttaac cagattagct
     2461 ctgagataaa tggaatccaa gaggctattt ctcaggctaa taataagcga agtacagcag
     2521 tttcacgtat tcatgatgct gaagataatt tgaaaacagc acagactaat ctcctgaact
     2581 cgcagattaa ggatgctgtg gatgcaacag ttagctttta tcaaacgcta tctgaaaaat
     2641 atggtgaaaa atattcaaaa atggcacagg aacttgctga taaatctaaa ggtaagaaaa
     2701 tcagcaatgt gaatgaagct ctagctgctt ttgagaaata caaggatgta ttaaataaga
     2761 aattcagcaa agcagaccgt gatgcaattt tcaatgcact ggaggcggtt aagtatgaag
     2821 actgggctaa gcatttagat cagtttgcca agtacttgaa gattacggga catgtttctt
     2881 ttggatatga tgtggtatct gatatcctaa aaattaagga tacaggtgac tggaagccgc
     2941 tatttcttac attagagaag aaagctgtag atgctggagt tagttatgtt gttgttttac
     3001 tttttagtgt gcttgctgga actacattag gtatctgggg gattgctatt gttacaggca
     3061 ttctatgtgc ctttattgat aagaataaac ttaatactat aaatgaggtg ttgggtattt
     3121 aattattctt tattgatata aacagtccta gcaatccaaa tgggattgct aggaccaaac
     3181 aaagtagatt gtatagcata aataggttta attttgccac gggggcatta tttaggtttt
     3241 ttctttttct gaaaaaatct ttctttatga acttaaaaaa tatgtgttca atagcatatt
     3301 ttgaatatgg gcatagaata gtgcttatca ctattgcgta tagcatctta tctgacgcta
     3361 ggaaataata cccttcgttg ttttttgtta taaggtatat atatataagt gcgcagtata
     3421 ggccaaacaa aatatttttt atgtagtatc ttaaactcat aaattaaacc tcgttatata
     3481 ttcttttcat tttataagga tcgagttatg aggaaaagat tttttgtggg aatattcgct
     3541 ataaacctcc ttgttggatg tcaggctaac tatatacgtg atgttcaggg agggactgtg
     3601 gctccatcat cttcttctaa attgacgggg atctctgttc agtagaaaag atcaaaggat
     3661 cttcttgaga tccttttttt ctgcgcgtaa tctgctgcct gtaaacgaaa aaaccgcctg
     3721 gggaggcggt ttgatcgaag gttaagtcag ttggggaact gcttaaccga ggtaactggc
     3781 ttcagcagag cgcagatacc aaatactgtc cttccagtgt agccgtagtc gggccactac
     3841 ttcaagaact ctgttgcacc atttgcgcca tcatcgctct gctaaccaag ttaccaacgg
     3901 ctgctgccag tggcgctaag tcgtgtctta ccgggttgga ctcaagacga tagttaccgg
     3961 ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa
     4021 cgacctacac cgagccgaga taccaacagc gtgagctatg agaaagcgcc acgcttcccg
     4081 aagggagaaa ggcggacagg tatccggtaa gcggcagggt cggaacagga gagcgcacga
     4141 gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct
     4201 ggcttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcct
     4261 gcggcgctgg cttcttccgg tgctttgctt tttgctcaca tgttctttcc ggctttatcc
     4321 cctgattctg tggataaccg tattaccgct tttgagtgag ctgacaccgc tcgccgcagt
     4381 cgaacgtccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgcct tatgtgacat
     4441 tttctcctta cgctctgttg tgccgttcgg catcctgtcc tgagcgttat ctctctgtgc
     4501 tattttctac ttcaaagcgt gtctggatgc tgttctggag ttcttctgcg agttcgtgca
     4561 gcttctcaca catggtagcc tgttcgtcag catcgagtgc gtccagcttt tcgagcagcg
     4621 tcaggctttg gctttttatg aatcctgcca tgttgagtac ggcttgctgc tgcttgttca
     4681 tcttttcgtt ttctccgttc tgtctgtcat ctgcgttgtg tgattatatc gcgtaccact
     4741 tttcgactgt tttaccgccg gtattctgcc gtctgacgct ttgacgggta tttctgcctg
     4801 acaatactgt cactgccaaa aaactgccgt gcctttgtcg gtaattcgaa cttgctgaca
     4861 ggacaggatg tgtaattgtt ataccgcgca tacatgcacg ctattacaat taccctggtc
     4921 agggctttgc cccgacaccc atgtcagata cggagccatg ttttatgaca aaacgaagtg
     4981 gaagtaatac gcgcaggcgg gctatcagtc gccc
//
