LOCUS       NZ_CP072862             4072 bp    DNA     linear   CON 11-FEB-2024
DEFINITION  Escherichia coli strain 184/2aE plasmid pEc184_4.
ACCESSION   NZ_CP072862
VERSION     NZ_CP072862.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18630606
            Assembly: GCF_018361365.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Santos Tufic-Garutti,S.D., de Araujo Longo,L.G., Fontana,H.,
            Garutti,L.H.G., de Carvalho Girao,V.B., Fuga,B., Lincopan,N., de
            Pinho Rodrigues,K.M. and Moreira,B.M.
  TITLE     OXA-181 carbapenemase carried on an IncX3 plasmid in high-risk
            Escherichia coli ST167 isolated from a traveler returning from
            Sub-Saharan Africa to Brazil
  JOURNAL   Diagn Microbiol Infect Dis 102 (1), 115570 (2022)
   PUBMED   34739936
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   dos Santos Tufic-Garutti,S., de Araujo Longo,L.G., Fontana,H., Groto
            Garutti,L.H., Brigido de Carvalho Girao,V., Fuga,B., Lincopan,N., de
            Pinho Rodrigues,K.M. and Meurer Moreira,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-APR-2021) Medical Microbiology, Universidade Federal
            do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bloco I,
            Lab I2-59, Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-MAR-2020
            Assembly Method                   :: UNICYCLER v. 0.4.8
            Assembly Name                     :: Ec184_2aE
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 09:00:58
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,845
            CDSs (total)                      :: 4,719
            Genes (coding)                    :: 4,486
            CDSs (with protein)               :: 4,486
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 71 of 233
            Pseudo Genes (incomplete)         :: 162 of 233
            Pseudo Genes (internal stop)      :: 43 of 233
            Pseudo Genes (multiple problems)  :: 42 of 233
            Pseudo Genes (short protein)      :: 4 of 233
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP072862.1.
            Bacteria and source DNA available from Laboratorio de Investigacao
            em Microbiologia Medica, Avenida Carlos Chagas Filho, 373, CCS,
            Bloco I, Lab I2-59 Cidade Universitaria, Rio de Janeiro, RJ,
            Brasil.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="184/2aE"
                     /isolation_source="Stool specimen"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc184_4"
                     /geo_loc_name="Brazil: Rio de Janeiro"
                     /lat_lon="22.95 S 43.17 W"
                     /altitude="15 m"
                     /collection_date="2017-12-10"
                     /collected_by="Instituto de Microbiologia Paulo de Goes"
     gene            complement(<1..565)
                     /locus_tag="J9158_RS23895"
                     /old_locus_tag="J9158_23780"
     CDS             complement(<1..565)
                     /locus_tag="J9158_RS23895"
                     /old_locus_tag="J9158_23780"
                     /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_052971458.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIK"
                     /name="replication initiation protein"
     gene            complement(1097..1351)
                     /gene="mobC"
                     /locus_tag="J9158_RS23900"
                     /old_locus_tag="J9158_23785"
     CDS             complement(1097..1351)
                     /gene="mobC"
                     /locus_tag="J9158_RS23900"
                     /old_locus_tag="J9158_23785"
                     /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_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1530..3689
                     /gene="mobQ"
                     /locus_tag="J9158_RS23905"
                     /old_locus_tag="J9158_23790"
     CDS             1530..3689
                     /gene="mobQ"
                     /locus_tag="J9158_RS23905"
                     /old_locus_tag="J9158_23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(3945..>4072)
                     /locus_tag="J9158_RS23910"
                     /old_locus_tag="J9158_23795"
                     /pseudo=""
     CDS             complement(3945..>4072)
                     /locus_tag="J9158_RS23910"
                     /old_locus_tag="J9158_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /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=3
                     /transl_table=11
                     /product="RepB family plasmid replication initiator
                     protein"
                     /name="RepB family plasmid replication initiator protein"
     Typing          complement(1353..1529)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1530..1888
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          complement(2..565)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.345"
                     /coverage="82.0"
                     /evalue="0.0"
     Typing          complement(3946..4072)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.399999999999999e-60"
     Typing          1444..3686
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttttattag tattttattt aagtctctga attgtttgta tttattttca atccctaaca
       61 ttgaacgaaa gtcattaaga gcaataattc tctctcccgt actgcggaat tgctggagga
      121 actcgtatat tcttatactg taactacttg ataaacctga tatgtttttt ataacaacgc
      181 gcgtgaattg ccccttcagt tgcgtcagat aaggcattac cgcgtcagaa aaggttattc
      241 gagccttggc ctcaccttta gcgtactgtg cccgatactg gatccagcgg aactcctcac
      301 gcttctcgtc attcttgaga atgatcgacc tgtcccataa acgatcgatc gcttcctgta
      361 actgaacctc ggcatttttc cgccccatgt cagggaatga atcaaaatat tccgcagcgg
      421 taatggtcat tgtcttttgc aattcagcat cagcaccaga tttcaatcga ctgatacaca
      481 gcaacagaaa acgttgttcc tgtagggtca acttgtagct ggcctcaacc aaagcattcg
      541 acttgtaggc aatcaagtcc gacatacaaa gatcccgttc aaatgtggtg atgctttaat
      601 gtgccccaca aataagaaat gtggaatatt tttttttata tcctcacatt tctgtgaata
      661 acaccttaaa ttcctccacc tttaccttaa attcctccac ctaaacacct taaattcctc
      721 cacctttacc ttaaattcct ccacatatac ctctataaca tattgatttt attaatgaat
      781 tttgacccta aaacaagtat taaaaacaag atcttaaaaa caagatctaa aaacttaacg
      841 gcgagcctgt ggataacttg gggcgctgaa aacaaaaaac caataaaaac aatgtgttgc
      901 aagaaagcag aattgcaagt tccgaatact ccccttccaa ccctgtggaa atccagtatt
      961 catgcgggtt cagcgcatat cacctaccga aaaaccgtgc gtatgtgctc aacctggcga
     1021 cggattcact tccgcttcct cgcccactcg ctcgctaacg ctcggtcgct ggggctgcgg
     1081 cgagcggacg atacaatcac tgtcctggca gcgcctccag ctcgttaatc agcggcagta
     1141 tgcgcgtcac atcagcctgt cgtgtcacct ctgccttcag gaactggagt aaccaggcac
     1201 gcaactgcac ctcctccggc tttctgacct ttgccagcaa tgctgcaccc acaacaacct
     1261 tctgcgctgt gtccaggctc cggctcttcg ccttcaggcg ctgtaatctc gcctcagcat
     1321 cagcaatctt ctgttcgagc gttctgctca tgatgtaact ccgtgcgcga tgaaaaatcg
     1381 cattttagcg cgtcactggt agtttaaaaa ctgagctggc ataatgcgcg acaaatcaca
     1441 aagtgcgcac ttatacaatc tccactccgt ttcgattgtg tgcgccctgc ggggctgaaa
     1501 gaaaactaca aaaaggcatt acggcagaaa tggcgattta tcatctcagc atgaaaatta
     1561 tctccagaag cagcggctac agcgccgtag cttccgctgc ctatcgttcc ggttcactga
     1621 tgcttgatga gcgtaccgga ctgactcacg actacacccg caaaagcggt gtggctgaag
     1681 ctgtgattct gacccccgcg acagcccctg cctggtgtac gaaccgtgcc gaactctgga
     1741 atgccgttga gaaggccgaa tgccggaaga actcacaact tgcgcgggaa attgaactcg
     1801 ctatcccccg tgaactgccg caggatgccg cacgggaaac cgttctcgcc tttgtcagag
     1861 aaaactttgt cagtcagggc atgattgctg atgtggcgtt ccatcacatg gataaaacaa
     1921 atccccatgc gcacatcatg ctgaccacga gggctgtcgg acctgctggg ttcggcggaa
     1981 aggtcaggga ctggaacgac cggacacatg ccgagacgtg gcgtgcatca tgggctgacc
     2041 atgcaaacag agcactggcg aacgccggtt atcaggaaga gatagaccat cgttcatacg
     2101 agcgacaggg gcttgagaaa acgcctggta ttcacctcgg aaagtctgcc tgtgcgatgg
     2161 aaacacgcgg tatcgaaaca gaacgcggcg aacagaatcg tctgattaac aggcttaacc
     2221 tggaaataca gatttcccgc actgaactca ggaacagcgg gctgacagag cctgcccgcc
     2281 gtgtggctga ccttctgaat atcgtgcttc ctgacaacgc aacttcgtac acactacgtg
     2341 acatcatcga agcgttgccg aaggacagta atgcggcatg gaaactcacc agtaatgcca
     2401 tgtcgatgat ggcagatatg caggcgacgc gcagacgctg ggaagagctg aacaccgaac
     2461 gaaaggaagc gatgagccat gctgccagcc tgaaaaaatc atcgccgttt tcgtccggtt
     2521 tttcccgtat tcccctgatg caatgggcgg caccggaata ccgtagcgaa cagggaaaaa
     2581 tccagtcgct gagccagcaa atggaaaaat tgcgacagca ttaccggaag gtggagaaac
     2641 aggacattcc cgcgagtcag acggcatttg aaaaacagtg gcagcagtgg ggggcatccg
     2701 gccttgcagc tctcagagtc cagttgctta aacgtgaaga ggaattgcgc cggaaggagc
     2761 aggaggatac agaacgtagt cgcgcggagc gacgagcgga acagctcagg aaaaatgaca
     2821 atgccgttat ggattcaggg gtactgagcg cagtcgttac ggggtatggc gaggccccca
     2881 tgcctggtaa cggggaaatg acctgttacc ttctgcttca caaccggaac ggagaataca
     2941 cgctctgggg gaacgagctg gagaaatacc gcaccagaat ctttgagcgt gttgatttaa
     3001 tgcgtgacag gagtggttat atctgtgacc gaagcgaaat cggtcaacat ccaccactgc
     3061 aacgtgttta ttcctctgcg acctttgagc aacttctgac gcaggtttgc cagacatggc
     3121 cgcaatatac ccgcaatctc cgccagccga agacatggcc ggagtctttc tgtcttggag
     3181 aagaccgcca gccagccatg ccatcactgg cagcaaggaa ggtggatttt acgcagggac
     3241 gtctgctacc gacgctgatg ccggtaatga gttctgtcga ccgggaaacc cgccagcttc
     3301 agcttttgct ggtcatgggc gtggatgact ctctgggcgg tgttgtccgg cttaatggta
     3361 cgctgtatcc cgcgtttgcc gttccctcag ccgataacag ccagctggtc atcagtgcac
     3421 tgaccgataa ggggttacgg tatgcagggt atggtgttgc cgtaaatcac gatgcagaca
     3481 gccacatatc acctgcgccg gaacttatgg agtttcatct gaaaacccgt gaggcaccgc
     3541 tttttgctgc cgtcaacaca ccagaaaaac agccggatca tctgttccgc tctctgggtt
     3601 tcaatcgtac ctgggatgaa tggcggcgcg aggaagatgc aagaacacac accaccgaga
     3661 ggagacatga tcgcggttgg tcacagtgaa tgtgaacaat attttgtttt gtttaacatc
     3721 gtgttatgtt cgtcgatgtt cttctatgtt catcgacagg gatgaatgca agaagcacac
     3781 acataatgca agcatagttt tgtttttccg cccccaaaaa ttgggggttc ttttttcgct
     3841 gcattagagc gcttttgacg caatttttca cttcaatagt accttcgcac tactaacaca
     3901 aaaaaaacgc agcagggagc gttttaggtg ccttaaaatc gattttagat cgtcatcttg
     3961 atctgtttgt cttccttgaa gcgaaaatgc agggctacaa ccgtgcgccc ctttttgatc
     4021 gtctcaaccg ttacagccag gtcgcttttt ttgttcagtt cgtcaacaca gg
//
