LOCUS       NZ_CP033765             4074 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain FDAARGOS_536 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP033765
VERSION     NZ_CP033765.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163231
            Assembly: GCF_003812625.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., 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  JOURNAL   Unpublished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 4074)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-NOV-2018) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: CA v. 8.2, SPAdes v. 3.6.0
            Genome Coverage                   :: 637.91065372549x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003812625.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 02:02:53
            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)                     :: 5,010
            CDSs (total)                      :: 4,893
            Genes (coding)                    :: 4,661
            CDSs (with protein)               :: 4,661
            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)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 83 of 232
            Pseudo Genes (incomplete)         :: 168 of 232
            Pseudo Genes (internal stop)      :: 40 of 232
            Pseudo Genes (multiple problems)  :: 52 of 232
            Pseudo Genes (short protein)      :: 1 of 232
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033765.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_536"
                     /isolation_source="Peripheral blood"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_536"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /collection_date="2016-04-02"
                     /collected_by="Children's National Hospital"
     gene            join(2867..4074,1..958)
                     /gene="mobQ"
                     /locus_tag="EGX93_RS25460"
                     /old_locus_tag="EGX93_25475"
     CDS             join(2867..4074,1..958)
                     /gene="mobQ"
                     /locus_tag="EGX93_RS25460"
                     /old_locus_tag="EGX93_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_061309377.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQKEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRAQL
                     LKREDELRRKELEDTERSRAERRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFESVDLIRGRSGYICDRSEIGQHPPLQRIYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            complement(1200..1901)
                     /locus_tag="EGX93_RS25465"
                     /old_locus_tag="EGX93_25480"
     CDS             complement(1200..1901)
                     /locus_tag="EGX93_RS25465"
                     /old_locus_tag="EGX93_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281396.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(2434..2688)
                     /gene="mobC"
                     /locus_tag="EGX93_RS25475"
                     /old_locus_tag="EGX93_25490"
     CDS             complement(2434..2688)
                     /gene="mobC"
                     /locus_tag="EGX93_RS25475"
                     /old_locus_tag="EGX93_25490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2690..2866)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2867..3225
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          complement(1202..1901)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.287"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          30..949
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.068"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          2781..4048
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.109"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 agatgaatta cgccggaagg agctggagga tacagaacgt agtcgcgcgg agcgacgagc
       61 ggaacagctc aggaaaaatg acaatgccgt tatggattca ggggtgctga gagcagtcgt
      121 tacggggtat ggcgaggctc ccatgcctgg taacggggaa atgacttgtt accttctgct
      181 tcacaaccgg aacggagaat acacgctctg ggggaacgag ctggagaaat accgcaccag
      241 gatctttgag agtgttgatt taatacgtgg caggagtggt tatatctgtg accgaagcga
      301 aatcggtcaa catccaccac tgcaacgtat ttattcctct gcgacctttg agcaacttct
      361 gacgcaggtt tgccagacat ggccgcaaca tacccgcaat ctccgccagc cgaagacatg
      421 gccggagtct ttctgtcttg gagaagaccg ccagccagcc atgccatcac tggcagcaag
      481 gaaggtggat tttacgcagg gacgtctgcc accgacgctg atgccggtca tgagttctgt
      541 cgaccgggaa acccgccagc ttcagctttt gctggtcatg ggcgtggatg actctctggg
      601 cggtgttgtc cggcttaatg gtacgctgta tcccgcgttt gccgttccct cagccgataa
      661 cagccagctg gttatcagtg cactgaccga taaggggtta cggtatgcag ggtatggtgt
      721 tgccgtaaat catgatgcag acagccacat atcacctgca ccggaactta tggagtttca
      781 tctgaaaacc cgtgaggcac cgctttttgc tgtcgtcaac acaccagaaa aacagccgga
      841 tcatctgttc cgctcgctgg gtttcaatcg tacctgggac gaatggcggc gcgaggaaga
      901 tgcacgaaca cacgccaccg agaggagacc tgatcgcggt tggtcacagg gaatgtgaac
      961 aatattttgt tttgtttaac atcgtgttat gttcgtcgat gttcatcgac agggatgaat
     1021 gcaagaagca cactcacata gcgcaaacat agttttgttt ttccgccccc aaaaattggg
     1081 ggttcttttt ttgctgcatc agagcgtttt tgacgcaact tttcacttca atagtacctt
     1141 cgcattcctg acacaagaaa aacgcgacag tgagcgtttt aggtgcctta aaatcgattc
     1201 tagatcgtca tcttgatctg tttgtcttcc ttgaagcgaa agtgcagggc tacaaccgtg
     1261 cgcccctttt tgatcgtctc aaccgttaca accagatcgc ttttttcgtt cagttcggcg
     1321 atggctggct tgattatcat cttattcaag tctttgaatt gttgatattt atcttcaacg
     1381 gcaagcatgg ttcggaaatc atcgatagct atcgttctgt caccggtgct gcggaactgc
     1441 tggagcagct cgtaaatgcg gatgctgtag gtgctggaga ggctggagac gttcttcacg
     1501 actacccgcg taaactgccc cttgagctgt gtcagatacg gcatgatggc atcggagaag
     1561 gtgatctcta ctttcgcctc acctttgaaa tactgcgccc ggtactgcac ccagcggaac
     1621 tcttctcgtt tttcctcgtt cttgatgatt actgacctgt cccagaggcg atctatcgct
     1681 tccttgagcc tagcttcagc gtgctgccgt cccatgtcag gaaaggcatc atgaaactct
     1741 gcagccgtga tggtcatggt tttttgttca tccggcgaag gggaatcttc tccggatttc
     1801 aggcggctga tacagaccag caggaagcgc tgttcctgca aagtgagctt gtagcttgcc
     1861 tcgataaggg cgtttgattt gtaagctatc agatctgaca tttcgcttgc tcgttgctat
     1921 tggtggcgtt tttttactgt acgccaccta tcatattggt ggaagttttt tttttgcaac
     1981 cccttttttc tgtggattac acccccaaaa gctccactta tcacccccaa aagctccacc
     2041 tatcaccccc aaaagctcca cctatcaccc ccaaaagctc cacctatctc gccagaacac
     2101 ctttaaaatc atgtggttac aagacctaaa aaggttttaa aaaaaaagat ctaaaaataa
     2161 gatcttaaaa acttaacggc gagcctgtgg ataacttggg gtgctgaaaa taaaaatcca
     2221 ataaaaacaa tgtgttgcaa aaaaccagga ttgaagattc cgaatacacc ccctccaacc
     2281 ctgtggaaat ccagtattca tgcgggttca gcgcatatca cctgtcgaaa aaccgtgcgt
     2341 atgtgctcaa catggcgact gattcacttc cgcttcctcg cccactcgct cgctaacgct
     2401 cggtcgctgg gctgcggcga gcggacgata caatcactgc tctggcagcg cctccagctc
     2461 gttaatcagc ggcagtattc gcgtcacatc agcctgccgt gtcacctctg ccttcaggaa
     2521 ctggagtaac caggctcgca actgcacttc ctccggcttt ctgacctttg ccagcaatgc
     2581 tgcacccaca atgaccttct gcgctgtgtc caggctccgg ctcttcgcct tcaggcgctg
     2641 taatctcgcc tcagcatcag caatcttctg ttcgagcgtt ctgctcatga tgtaactcca
     2701 tgcgcgatga aaaatcgcat tttagcgcgt cactggtagt ttaaaaactg agctggcata
     2761 atgcacggca aatcacgaag tgcgcactta tacaatctcc actccgtttc gattgtgtgc
     2821 gccctgcggg gctgaaagaa aactgcaaaa aggcattacg gcagaaatgg cgatttatca
     2881 tctcagtatg aaaatcatct ccagaagcaa cggctacagc gccgttgctt ctgctgccta
     2941 tcgttctggt tcactaatgc ttgatgagcg taccggactg actcacgact acacccgcaa
     3001 aagcggtgtg gctgaggctg tgattctgac ccccgcgaca gcccctgcct ggtgtacgaa
     3061 ccgtgccgaa ctctggaatg ccgttgagaa ggccgaacgc cggaagaact cacaacttgc
     3121 gcgggaaatt gaactcgcca tcccccacga actgccgcag gatgccgcac gggaaaccgt
     3181 tctcgccttt gtcagagaaa actttgtcag tcagggcatg attgctgatg tggcgttcca
     3241 tcacatggat aaaacaaatc cccatgcgca cattatgctg accacgaggg ctgtcggacc
     3301 tgcggggttc ggcggaaagg tcagggactg gaacgaccgg acacatgccg agacgtggcg
     3361 tgcatcatgg gctgaccatg caaacagggc actggcgaac gccggttatc agaaagagat
     3421 agaccatcgt tcatacgagc gacaggggct tgagaaaacg ccgggtattc acctcggaaa
     3481 gtctgcctgt gcgatggaaa cacgcggtat cgaaacagaa cgcggcgaac agaatcgtct
     3541 gattaacagg cttaacctgg aaatacagat ttcccgcacc gaactcagga acagcgggct
     3601 gacagagcct gcccgccgtg tggctgacct tctgaatatc gggcttcctg acaacgcaac
     3661 ttcgtacaca ctacgtgaca tcatcgaagc gttgccgaag gacagtaacg cggcatggaa
     3721 actcaccagt aacgccatgt cgatgatggc agatatgcag gcgacgcgca gacgctggga
     3781 agagctgaac accgaacgaa aggaagcgat gagccatgct gccagcctga aaaaatcatc
     3841 gccgttttcg tccggttttt cccgtattcc cctgatgcaa tgggctgcac cggaataccg
     3901 tagtgagcag ggaaaaatcc agtctctgag ccagcaaatg gaaaaattgc gacagcatta
     3961 ccggaaggtg gagaaacagg acattcccgc gagtcagacg gcatttgaaa aacagtggca
     4021 gcagtggggg gaatccggcc ttgcagctct cagagcccag ttgcttaaac gtga
//
