LOCUS       NZ_CP070005             4760 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1300 plasmid unnamed9.
ACCESSION   NZ_CP070005
VERSION     NZ_CP070005.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357442
            Assembly: GCF_016903915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4760)
  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  JOURNAL   Unpublished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 4760)
  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                   :: 1255.12x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:03:37
            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)                     :: 5,439
            CDSs (total)                      :: 5,322
            Genes (coding)                    :: 5,075
            CDSs (with protein)               :: 5,075
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 94 of 247
            Pseudo Genes (incomplete)         :: 157 of 247
            Pseudo Genes (internal stop)      :: 46 of 247
            Pseudo Genes (multiple problems)  :: 48 of 247
            Pseudo Genes (short protein)      :: 4 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070005.1.
            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..4760
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1300"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1300"
                     /db_xref="taxon:562"
                     /plasmid="unnamed9"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(82..501)
                     /locus_tag="I6K30_RS26825"
                     /old_locus_tag="I6K30_26830"
     CDS             complement(82..501)
                     /locus_tag="I6K30_RS26825"
                     /old_locus_tag="I6K30_26830"
                     /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(582..1001)
                     /locus_tag="I6K30_RS26830"
                     /old_locus_tag="I6K30_26835"
     CDS             complement(582..1001)
                     /locus_tag="I6K30_RS26830"
                     /old_locus_tag="I6K30_26835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001711305.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001329498.1"
                     /translation="MAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRREFETSE
                     LIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQAQDTERR
                     RQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            1279..2844
                     /locus_tag="I6K30_RS26835"
                     /old_locus_tag="I6K30_26840"
     CDS             1279..2844
                     /locus_tag="I6K30_RS26835"
                     /old_locus_tag="I6K30_26840"
                     /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_083575038.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELVKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(2841..3182)
                     /locus_tag="I6K30_RS26840"
                     /old_locus_tag="I6K30_26845"
     CDS             complement(2841..3182)
                     /locus_tag="I6K30_RS26840"
                     /old_locus_tag="I6K30_26845"
                     /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            3230..3367
                     /locus_tag="I6K30_RS26845"
                     /old_locus_tag="I6K30_26850"
     CDS             3230..3367
                     /locus_tag="I6K30_RS26845"
                     /old_locus_tag="I6K30_26850"
                     /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(4209..4403)
                     /locus_tag="I6K30_RS26850"
                     /old_locus_tag="I6K30_26855"
     CDS             complement(4209..4403)
                     /locus_tag="I6K30_RS26850"
                     /old_locus_tag="I6K30_26855"
                     /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"
     gene            4687..>4760
                     /locus_tag="I6K30_RS26855"
                     /old_locus_tag="I6K30_26860"
                     /pseudo=""
     CDS             4687..>4760
                     /locus_tag="I6K30_RS26855"
                     /old_locus_tag="I6K30_26860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-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"
     Typing          4439..4678
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.585"
                     /coverage="100.0"
                     /evalue="3.54e-121"
     Typing          complement(3651..4178)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.569"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 ctctttttgc ggtgtctgcg tcagaatcgc gttcagcgcg tttcagtggt gcgtacaatt
       61 aagggattat ggtaaatcca cttactgtct gccctcgtag ccatcgagat aaaccgcaga
      121 aatcgtgtca gccagcagcc tggatttttt cggggtaagg tctttgctgc ggtaatcagt
      181 acccgcaaat tgagttgtgc cccggagtga gtttaaaaat tcctggctgt gaaactgttg
      241 aatgcgttgt tgcacatcac tccgtgattt tcctgtcgct ttatctttag ctcccatatc
      301 ccagaactgc cgaaaaaaag gcaccatcat tcgtgttgtg tcggcttttt gggtggaaaa
      361 gttgggatca aaaccgtcat cagaagcata tacgtaatgc cgggtatgtt gttccacgct
      421 gccctttggg gtacaggctg tgagagctac tgttgctgtt atcatggcga taagacaaag
      481 tttgtttccg gtacgtctca tgagtgtctc cctaccttaa agtatttatt ctcggtgagt
      541 tattatccga agattatctt atcatcagtt tctgagcgcg ttcagtgacc gaacagcctg
      601 gaccagaatc cccgtttctt ttcctgctcc agagcctgcc tgagctgggc tatctcattc
      661 tgtagctgtt tccgttctgc ttcctggcgc cggcgctccg tatcctgggc ttgtttatcc
      721 tcaagcatca gcgtcaggca ttgtttcagc tcattcagtt cccggagaat gcgttctgtc
      781 tgctgatcat gaggtttttc tgagtgtcct tgagtgtgcc tttctggtgt ctcattccgc
      841 tttaattcgc cgtatgcccg gatcagttca ctggtttcaa actcccgtcg tccgtcctgg
      901 ctggtacggt aactgacaag acctgagcgc atatcacggt aaaactgtga acgcgatctt
      961 ccagtcattt tcagtgcgtc ccggagtgtg tgccatgcca taaagttaca gtgtcccata
     1021 ggtgtctcat ctcatggttt cagtaaaaca taatgaggtc tgagaacggt aatgtttgtg
     1081 ctggtttttg tggcatcggg tggaaatagc acgtggtgtg ggtggctgtt tttttgatcg
     1141 ttttcacaaa aatgaaaatc cacagggttg acagggaaaa tacagcggcg taatttcaaa
     1201 ctgtatataa aaccagtgat tatatataca gtatattgct tttaactatt tgtttttaat
     1261 gtcaaagagg attttataat ggaaacagct gtagcgtact ataaagatgg tgttccttat
     1321 gatgataagg ggcaggtaat cattactctt ttgaatggta atccagacgg gagtggctct
     1381 ggcggtggtg gtggaactgg aggtagcaaa agtgaaagtt ctgcagccat tcatgccaca
     1441 gctaaatggt ctactgctca attgaagaaa acgcaggcag aacaggctgc ccgagcaaaa
     1501 gctgccgcag aagcacaggc taaagcaaaa gcaaaccggg atgcgctgac tcaacatctg
     1561 aaggatattg tgaatgaggc gcttcgccat aattccactc atccggaggt tattgacctg
     1621 gctcatgcca ataatgcagc gatgcaggca gaagcagagc ggttgcgcct tgcaaaagca
     1681 gaagaaaaag cccgtaaaga agcggaagct gcggaaaagg cttttcagga agcagaacaa
     1741 cgacgtaaag agatagagaa ggagcaggct gaaacagaac gccaattgaa actggctgag
     1801 gatgaagaga aacgcctggc agcattgagt gaagaggccc gggctgtgga ggtggcacaa
     1861 aaaaatcttg ctgctgcaca atctgagctg gtgaaagtgg atgaagagat taatacgctc
     1921 aatacccgtt taagctccag tattcatgcc cgtgatgcag aaacgaatac gctgtccgga
     1981 aaacgaaatg agttggatca ggcatctgct aaatataaag aactggatga aagggttaaa
     2041 cttttatctc ctagggcgaa tgatccgctt cagagccgtc ctttttttga ggccaccaga
     2101 ctacgggcga gagctggtga tgagatggag gaaaaacaaa agcaggtaac agcatcagaa
     2161 acgcgtctta accagattag ctctgagata aatggaatcc aagaggctat ttctcaggct
     2221 aataataagc gaagtacagc agtttcacgt attcatgatg ctgaagataa tttgaaaaca
     2281 gcacagacta atctcctgaa ctcgcagatt aaggatgctg tggatgcaac agttagcttt
     2341 tatcaaacgc tatctgaaaa atatggtgaa aaatattcaa aaatggcaca ggaacttgct
     2401 gataaatcta aaggtaagaa aatcagcaat gtgaatgaag ctctagctgc ttttgagaaa
     2461 tacaaggatg tattaaataa gaaattcagc aaagcagacc gtgatgcaat tttcaatgca
     2521 ctggaggcgg ttaagtatga agactgggct aagcatttag atcagtttgc caagtacttg
     2581 aagattacgg gacatgtttc ttttggatat gatgtggtat ctgatatcct aaaaattaag
     2641 gatacaggtg actggaagcc gctatttctt acattagaga agaaagctgt agatgctgga
     2701 gttagttatg ttgttgtttt actttttagt gtgcttgctg gaactacatt aggtatctgg
     2761 gggattgcta ttgttacagg cattctatgt gcctttattg ataagaataa acttaatact
     2821 ataaatgagg tgttgggtat ttaattattc tttattgata taaacagtcc tagcaatcca
     2881 aatgggattg ctaggaccaa acaaagtaga ttgtatagca taaataggtt taattttgcc
     2941 acgggggcat tatttaggtt ttttcttttt ctgaaaaaat ctttctttat gaacttaaaa
     3001 aatatgtgtt caatagcata ttttgaatat gggcatagaa tagtgcttat cactattgcg
     3061 tatagcatct tatctgacgc taggaaataa tacccttcgt tgttttttgt tataaggtat
     3121 atatatataa gtgcgcagta taggccaaac aaaatatttt ttatgtagta tcttaaactc
     3181 ataaattaaa cctcgttata tattcttttc attttataag gatcgagtta tgaggaaaag
     3241 attttttgtg ggaatattcg ctataaacct ccttgttgga tgtcaggcta actatatacg
     3301 tgatgttcag ggagggactg tggctccatc atcttcttct aaattgacgg ggatctctgt
     3361 tcagtagaaa agatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc
     3421 ctgtaaacga aaaaaccgcc tggggaggcg gtttgatcga aggttaagtc agttggggaa
     3481 ctgcttaacc gaggtaactg gcttcagcag agcgcagata ccaaatactg tccttccagt
     3541 gtagccgtag tcgggccact acttcaagaa ctctgttgca ccatttgcgc catcatcgct
     3601 ctgctaacca agttaccaac ggctgctgcc agtggcgcta agtcgtgtct taccgggttg
     3661 gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc
     3721 acacagccca gcttggagcg aacgacctac accgagccga gataccaaca gcgtgagcta
     3781 tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg
     3841 gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt
     3901 cctgtcgggt ttcgccacct ctggcttgag cgtcgatttt tgtgatgctc gtcagggggg
     3961 cggagcctat ggaaaaacgc ctgcggcgct ggcttcttcc ggtgctttgc tttttgctca
     4021 catgttcttt ccggctttat cccctgattc tgtggataac cgtattaccg cttttgagtg
     4081 agctgacacc gctcgccgca gtcgaacgtc cgagcgtagc gagtcagtga gcgaggaagc
     4141 ggaagagcgc cttatgtgac attttctcct tacgctctat tgtgccgttc ggcatcctgt
     4201 cctgagcgtt atctctctgt gctattttct acttcaaagc gtgtctggat gctgttctgg
     4261 agttcttctg cgagttcgtg cagcttctca cacatggtag cctgttcgtc agcatcgagt
     4321 gcgtccagct tttcgagcag cgtcaggctt tggcttttta tgaatcctgc catgttgagt
     4381 acggcttgct gctgcttgtt catcttttcg ttttctccgt tctgtctgtc atctgcgttg
     4441 tgtgattata tcgcgtacca cttttcgact gttttaccgc cggtattctg ccgtctgaag
     4501 ctttgacggg tatttctgcc tgacaatact gtcactgcca aaaaactgcc gtgcctttgt
     4561 cggtaattcg aacttgctga caggacagga tgtgtaattg ttataccgcg catacatgca
     4621 cgctattaca attaccctgg tcagggcttt gccccgacac ccatgtcaga tacggagcca
     4681 tgttttatga caaaacgaag tggaagtaat acgcgcaggc gggctatcag tcgccctgtt
     4741 cgtctgacgg cagaagaaga
//
