LOCUS       NZ_CP070079             5570 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1371 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP070079
VERSION     NZ_CP070079.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357513
            Assembly: GCF_016904255.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5570)
  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  JOURNAL   Unpublished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 5570)
  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                   :: 751.4x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:04:03
            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)                     :: 4,937
            CDSs (total)                      :: 4,819
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 68 of 181
            Pseudo Genes (incomplete)         :: 109 of 181
            Pseudo Genes (internal stop)      :: 39 of 181
            Pseudo Genes (multiple problems)  :: 34 of 181
            Pseudo Genes (short protein)      :: 4 of 181
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070079.1.
            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..5570
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1371"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1371"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(<98..328)
                     /locus_tag="I6L01_RS24820"
                     /pseudo=""
     CDS             complement(<98..328)
                     /locus_tag="I6L01_RS24820"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(537..860)
                     /locus_tag="I6L01_RS24370"
                     /old_locus_tag="I6L01_24375"
     CDS             complement(537..860)
                     /locus_tag="I6L01_RS24370"
                     /old_locus_tag="I6L01_24375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            924..1115
                     /locus_tag="I6L01_RS24375"
                     /old_locus_tag="I6L01_24380"
     CDS             924..1115
                     /locus_tag="I6L01_RS24375"
                     /old_locus_tag="I6L01_24380"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2138..3094)
                     /locus_tag="I6L01_RS24380"
                     /old_locus_tag="I6L01_24385"
     CDS             complement(2138..3094)
                     /locus_tag="I6L01_RS24380"
                     /old_locus_tag="I6L01_24385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_223673566.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVYKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            3165..4304
                     /gene="dcm"
                     /locus_tag="I6L01_RS24385"
                     /old_locus_tag="I6L01_24390"
     CDS             3165..4304
                     /gene="dcm"
                     /locus_tag="I6L01_RS24385"
                     /old_locus_tag="I6L01_24390"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="WP_033550328.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAIMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            complement(4671..4904)
                     /locus_tag="I6L01_RS24390"
                     /old_locus_tag="I6L01_24395"
     CDS             complement(4671..4904)
                     /locus_tag="I6L01_RS24390"
                     /old_locus_tag="I6L01_24395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4911..5429)
                     /locus_tag="I6L01_RS24395"
                     /old_locus_tag="I6L01_24400"
     CDS             complement(4911..5429)
                     /locus_tag="I6L01_RS24395"
                     /old_locus_tag="I6L01_24400"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     Typing          complement(1201..1288)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          1312..1857
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.353"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..547)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.451"
                     /coverage="99.0"
                     /evalue="2.02e-115"
     Typing          complement(4568..5568)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.015"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggtaaagtgc gtctataccg cgtgtaacgc tctcagcaag tgcctgtttc gtttccggca
       61 ggttatcagg aagagtcagc gtccggcggt tctccggggc gttggggtca tgcagtccgt
      121 aatggtgatt caccagcgtc tgccaggcat caattctcgg cctgtctgcg cggtcgtagt
      181 acggctggag acgttttccg gtctgtagct ccatgttcgg aatgacaaaa ttcagctcaa
      241 gccgtccctt gtcctggtgc tccacccaca gaatgctgta ctgatttttt tcgagaccgg
      301 gcatcagtac acgctcaaag ctcgccatca ctttttcacg tcctcccggc ggcagctcct
      361 tctccgcgaa cgacagaaca ccggacgtgt atttcttcgc aaatggcgtg gcatcgatga
      421 gttcccggac ttcttccgga ttaccctgaa gcaccgttgc gccttcgcgg ttacgctccc
      481 tccccagcag gtaatcaacc ggaccactgc caccaccttt tcccctggca tgaaatttaa
      541 ctatcatccc gcgccccctg ttccctgacg gccagacgca gccggcgcag ctcatccccg
      601 atggccatca gtgcggccac cacctgaacc cggtcaccgg aagaccactg cccgctgttc
      661 accttacggg ctgtctgatt caggttattt ccgatggcgg ccagctgacg cagtaacggc
      721 ggtgccagtg tcggcagttt cccggaacgg gcaaccggct cccccaggca gacccgccgc
      781 atccataccg ccagttgttt accctcacag cgttcaagta acctggcatg ttcatcatca
      841 gtaacccgta tcgtgagcat cctctcgcgt ttcatcggta ttattacccc atgaacagaa
      901 atccccctta cacggaggca tcagtgacta aacaggaaaa aacagccctt aacatggcgc
      961 gctttatcag aagccagaca ttaacgctgc tggaaaagct caacgaactg gacgcggatg
     1021 aacaggcaga catctgtgaa tcgcttcacg accacgccga tgagctttac cgcagctgcc
     1081 tcgcacgttt cggggatgac ggtgaaaacc tctgacacat gcagctccca gagacggtca
     1141 cagcttgtct gtgagcggat gccgggagca gacaagcccg tcagggcgcg tcagcaggtt
     1201 ttagcgggtg tcggggcgca gccctgaccc agtcacgtag cgatagcgga gtgtatactg
     1261 gcttaactat gcggcatcag tgcggattgt atgaaaagca cgccatgccg ggtgtgaaat
     1321 gccgcacaga tgcgtaagga gaacataccg catcaggcgc tcttccgctt cctcgctcac
     1381 tgactcgctg cgctcggtcg ttcggctgcg gcaagcggtg ccggctcact caaaggcgga
     1441 aatacggtta tccacagaat caggggataa ggccggaaag aacatgtgag taaaaaggca
     1501 aagggcaaca aaaggccgcg ccgctggcgt ttttccatag gctccgcccc cctgacgagc
     1561 atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc
     1621 aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg
     1681 gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgtt
     1741 ggtatctcgg cccggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg
     1801 ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccagtaagac
     1861 acgccttaac gccactggca gcagccactg gtaaccggat tagcagagcg agatttatcc
     1921 agatgcttac agagttcttg aagtgatggc ctaactacgg ctacactgga aggacagtat
     1981 ttggtatctg tgctctgctg aagccagatt acctcggtta gataatctgc caggattagc
     2041 taaccttcga aaaaaccacc tgccagggtg gttttttcgt ttacaggtcc aagattacgc
     2101 gcagaaaaaa aggatctcaa gagatccttt tagtttttta gtcaaaaaga gcactaagcc
     2161 tatttctata ataattaaca acataaggga aatcactata tttttctatt tgttttaata
     2221 ttgactgttg aatttcctct ttttcagagt ctgtgtaact tacattattc cactttcttg
     2281 ataattccat tgctgactgt agcatatctt caaaggttag caccctatta ttatttttat
     2341 atttgaaatt tttattttct atcgtcgtta caacgaccac attagcctcg tacaatatat
     2401 ttattgtctc ctcgctaaaa gaatcatcta gtgtagctag atacatttct ctaattcctg
     2461 ttctattaac ctcttcaggt acttcttgcc atcgctccct cagcgttgtt ttagcggaaa
     2521 tcaacattgt atttcttttg ttagatgtgt actggactac acctggcata acaagatcta
     2581 caagtttacc tatttggttt ttttgaaaaa atgacttccc aatagccccc tgcacatcaa
     2641 caggaattcc tgcccccatc attaatagct caagaataga ctcaaactct tttcctgccc
     2701 tgctacgtct ggattgagtg ttagacagtg ccaaatcata tatgtgtgta gggtattcca
     2761 tcgtaaaatc acgaatggca tcataaggac tcatatcttt tattctttct tcatcaataa
     2821 gatatgataa cattcttgtt gtgaattctt tttcaaatgg ttcaaattct ttccaacagt
     2881 tttttctcat tgcaattata tattcacttg gattattcaa aaaataatca ctattttttt
     2941 gatcataccc taaatcacaa aatgttttat aaaccaaagc aaatggcgta ataaaatgcg
     3001 actttctctc tttagaaatt agagttttaa attcaccagg actcaatctt tgcataaaaa
     3061 ataacctttt atatctactt gaaagttttt tcatgcacgt tcataattgg aatcaaaaca
     3121 ggacaaattg tcctaaaacc aacacttaat tctggtagac atgcatgact gataatatcg
     3181 cagcaacaat caaaggaaaa agagaaagac ttcatatgac tcaaaaagag tttgcagacg
     3241 cccttggtct ttcaaaatat ggagacagaa ccataagaag atgggagcgc ggggaaacaa
     3301 aacctactgg ggcggaacta aaagcaatta tggactttcc agacacacca ccttacccaa
     3361 acaacgagaa tggcagatat cgcatgatcg atttatttgc tggaatcggt ggaaccagac
     3421 ttggatttca tcaaactaac gctgtaaatg ttgttttttc cagcgaatgg gataagtttg
     3481 ctcaaaagac atatcatgca aattatggtg atttccctga tggggacata acaaaaatcg
     3541 atgaaaaaga tattcctgat catgaaattc ttgtcggtgg gtttccttgc gtagcattct
     3601 ctcaagcagg gctcaaaaaa ggatttaatg atacaagagg aactttgttt tttgatatag
     3661 caaggataat aaaggaaaaa aaacctcatg cttttttact tgaaaatgta aaaaacttgc
     3721 taggacatga taaaggtaga actttttcaa taataaaaaa cacacttgaa gaattgaatt
     3781 acactgtgta ttacaatatc ttcgctgcaa aagactttgg tgttccacaa aatagagaac
     3841 gcatatacat tgtaggcttt aataaagaaa aagtaagaaa tcatgaacat tttacttttc
     3901 caaccccgtt aaaaacaaaa acaagagttg gagatattct tgaaaagagc gtagacaata
     3961 aatatacgct atcagatgcg ctctggaatg gacaccaacg caggaaactt gtaaatgcag
     4021 cagccggtaa aggctttggg tatggtttat ttaatgaaaa tagcccatat actaatacca
     4081 taagtgcgag gtactataaa gatggtagtg aaatattaat agagcaaaaa ggaagtaacc
     4141 caagaaaaat aactccgcgg gaagcgtcaa gacttcaagg gtttcctagt gattttatta
     4201 tccctgtatc ggatacacag gcttataagc aatttgggaa ttcagtcgca gtccctgtta
     4261 tcaatgcaat agcagaaaaa atcatatcga ccttagattc ataaactaag tcataaggac
     4321 acaatgcggc ccagaatcca attacccccc ccatatggat ttaccataac gtcgcattac
     4381 gcgcaccgct gaaacgcgtt cagcgcgatc acggcagcag acaggtaaaa atggcaacaa
     4441 accacccgaa aaactgccgc gatcgcgcct gataaatttt aaccgcatga atacctatgc
     4501 aaccagatgg tacaggccac attaacccct cttaatccac tgaagctgcc atttttcatg
     4561 gtttcaccat cccagcgaag gaccatccag cgtgcgttcc tgtatttccg gctgacgctc
     4621 ccgttccagg gataacgcat gttcgcgctc ctgtatcagc cgttcctctc ttatctccag
     4681 ttctcgctgt ataactggct caagcgttct gtctgctcgc tcaagtgctg cacctgctga
     4741 ctcaactgca tgacccgctc gttcagcatc gcgttgtccc gttgcgtaag cgaaaacatc
     4801 ttctgcaatt ccacgaaggc gctctcccat tcgctcagcc gctgcatata gtcctgttgc
     4861 agctgctcta aggcgttcag caaatgtatt tccagctctg tcactctgtg tcactccttc
     4921 agatgtaccc actctttccc ctgaaaggga atcacctccg ctgatttccc gtacggaagg
     4981 acaaggaatt tcctgttccc gtcctgcaca aactccacgc cccatgtctt cgcgttcagt
     5041 ttctgcaatg tctcttcctg cttcctgatt tcttccaggt tcgtctgtat ccgtccgcca
     5101 agataccaga gcgtcccgcc actcgcggta aacaggagaa agactatccc cagtaacatc
     5161 atgcccgtat tccctgccag ctttaacacg tccttcctgt gctgcatcat cgcctctttc
     5221 accccttccc ggtgtttttc cagcgatttc tctgtcgagg ctgtgaacag ggctatagcg
     5281 tctctgattt tcgtctcgtt tgaggtcaca gcctcgctga cagactcgcc gagcttcctg
     5341 aactcgtcgt tcagcatttt ctctgtagat tcggctctct ctttcagctt tttctcgaac
     5401 tccgcgcccg tctgtaaaag attgctcata aaacgctcct ttcagtctga tattcctccc
     5461 gccgttcggg tctgcaatgc tgatactgct tcgcgtcacc ctgaccactt caagccccgc
     5521 ctctgtgagc gcctgaatca catcctgacg gccttttatc tctccggcat
//
