LOCUS       NZ_CP008718             4073 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli strain ST648 isolate Pleural Effusion of Patients
            with Empyema Thoracis plasmid pEC648_4, complete sequence.
ACCESSION   NZ_CP008718
VERSION     NZ_CP008718.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02800875
            Assembly: GCF_001485455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  AUTHORS   Gao,Z.
  TITLE     Complete Genome Sequence of Multiple Antibiotic Resistant
            Escherichia coli Isolated from Pleural Effusion of Patients with
            Empyema Thoracis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4073)
  AUTHORS   Gao,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUN-2014) Department of Respiratory and Critical care
            medicine, Peking University People's hospital, Xizhimen South
            Street, Beijing, Beijing 100101, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Newbler v. 2.3; Consed
            Genome Coverage                   :: 40x; 350x
            Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001485455.1-RS_2024_06_12
            Annotation Date                   :: 06/12/2024 02:11:21
            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)                     :: 5,056
            CDSs (total)                      :: 4,958
            Genes (coding)                    :: 4,655
            CDSs (with protein)               :: 4,655
            Genes (RNA)                       :: 98
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 303
            CDSs (without protein)            :: 303
            Pseudo Genes (ambiguous residues) :: 0 of 303
            Pseudo Genes (frameshifted)       :: 162 of 303
            Pseudo Genes (incomplete)         :: 139 of 303
            Pseudo Genes (internal stop)      :: 50 of 303
            Pseudo Genes (multiple problems)  :: 41 of 303
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP008718.1.
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ST648"
                     /isolate="Pleural Effusion of Patients with Empyema
                     Thoracis"
                     /isolation_source="Pleural Effusion"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC648_4"
                     /geo_loc_name="China:Beijing"
                     /lat_lon="39.93 N 116.35 E"
                     /collection_date="2009-05-24"
                     /collected_by="Dezhi Li"
     gene            complement(join(2489..4073,1..581))
                     /gene="mobQ"
                     /locus_tag="FH07_RS25715"
     CDS             complement(join(2489..4073,1..581))
                     /gene="mobQ"
                     /locus_tag="FH07_RS25715"
                     /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_001029349.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQKEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRAQL
                     LKREDELRRKELEDTERSRAERRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFESVDLIRDRSGYICDRSEIGQHPPLQRIYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            760..1014
                     /gene="mobC"
                     /locus_tag="FH07_RS25720"
                     /old_locus_tag="FH07_00750"
     CDS             760..1014
                     /gene="mobC"
                     /locus_tag="FH07_RS25720"
                     /old_locus_tag="FH07_00750"
                     /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"
     gene            1546..2247
                     /locus_tag="FH07_RS25725"
                     /old_locus_tag="FH07_00755"
     CDS             1546..2247
                     /locus_tag="FH07_RS25725"
                     /old_locus_tag="FH07_00755"
                     /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_060684539.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAEVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(224..582)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          583..759
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1547..2246
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.144"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(4..668)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.297"
                     /coverage="99.0"
                     /evalue="9.45e-141"
     Typing          complement(2499..4072)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.524"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ccctgtcgct cgtatgaacg atggtctatc tctttctgat aaccggcgtt cgccagtgcc
       61 ctgtttgcat ggtcagccca tgatgcacgc cacgtctcgg catgtgtccg gtcgttccag
      121 tccctgacct ttccgccgaa ccccgcaggt ccgacagccc tcgtggtcag cataatgtgc
      181 gcatggggat ttgttttatc catgtgatgg aacgccacat cagcaatcat gccctgactg
      241 acaaagtttt ctctgacaaa ggcgagaacg gtttcccgtg cggcatcctg cggcagttcg
      301 tgggggatgg cgagttcaat ttcccgcgca agttgtgagt tcttccggcg ttcggccttc
      361 tcaacggcat tccagagttc ggcacggttc gtacaccagg caggggctgt cgcgggggtc
      421 agaatcacag cctcagccac accgcttttg cgggtgtagt cgtgagtcag tccggtacgc
      481 tcatcaagca ttagtgaacc agaacgatag gcagcagaag caacggcgct gtagccgttg
      541 cttctggaga tgattttcat actgagatga taaatcgcca tttctgccgt aatgcctttt
      601 tgcagttttc tttcagcccc gcagggcgca cacaatcgaa acggagtgga gattgtataa
      661 gtgcgcactt cgtgatttgc cgtgcattat gccagctcag tttttaaact accagtgacg
      721 cgctaaaatg cgatttttca tcgcgcatgg agttacatca tgagcagaac gctcgaacag
      781 aagattgctg atgctgaggc gagattacag cgcctgaagg cgaagagccg gagcctggac
      841 acagcgcaga aggtcattgt gggtgcagca ttgctggcaa aggtcagaaa gccggaggaa
      901 gtgcagttgc gagcctggtt actccagttc ctgaaggcag aggtgacacg gcaggctgat
      961 gtgacgcgaa tactgccgct gattaacgag ctggaggcgc tgccagagca gtgattgtat
     1021 cgtccgctcg ccgcagccca gcgaccgagc gttagcgagc gagtgggcga ggaagcggaa
     1081 gtgaatcagt cgccatgttg agcacatacg cacggttttt cgacaggtga tatgcgctga
     1141 acccgcatga atactggatt tccacagggt tggagggggt gtattcggaa tcttcaatcc
     1201 tggttttttg caacacattg tttttattgg atttttattt tcagcacccc aagttatcca
     1261 caggctcgcc gttaagtttt taagatctta tttttagatc ttttttttaa aaccttttta
     1321 ggtcttgtaa ccacatgatt ttaaaggtgt tctggcgaga taggtggagc ttttgggggt
     1381 gataggtgga gcttttgggg gtgataggtg gagcttttgg gggtgataag tggagctttt
     1441 gggggtgtaa tccacagaaa aaaggggttg caaaaaaaaa acttccacca atatgatagg
     1501 tggcgtacag taaaaaaacg ccaccaatag caacgagcaa gcgaaatgtc agatctgata
     1561 gcttacaaat caaacgccct tatcgaggca agctacaagc tcactttgca ggaacagcgc
     1621 ttcctgctgg tctgtatcag ccgcctgaaa tccggagaag attccccttc gccggatgaa
     1681 caaaaaacca tgaccatcac ggctgcagag tttcatgatg cctttcctga catgggacgg
     1741 cagcacgctg aagctaggct caaggaagcg atagatcgcc tctgggacag gtcagtaatc
     1801 atcaagaacg aggaaaaacg agaagagttc cgctgggtgc agtaccgggc gcagtatttc
     1861 aaaggtgagg cggaagtaga gatcaccttc tccgatgcca tcatgccgta tctgacacag
     1921 ctcaaggggc agtttacgcg ggtagtcgtg aagaacgtct ccagcctctc cagcacctac
     1981 agcatccgca tttacgagct gctccagcag ttccgcagca ccggtgacag aacgatagct
     2041 atcgatgatt tccgaaccat gcttgccgtt gaagataaat atcaacaatt caaagacttg
     2101 aataagatga taatcaagcc agccatcgcc gaactgaacg aaaaaagcga tctggttgta
     2161 acggttgaga cgatcaaaaa ggggcgcacg gttgtagccc tgcactttcg cttcaaggaa
     2221 gacaaacaga tcaagatgac gatctagaat cgattttaag gcacctaaaa cgctcactgt
     2281 cgcgtttttc ttgtgtcagg aatgcgaagg tactattgaa gtgaaaagtt gcgtcaaaaa
     2341 cgctctgatg cagcaaaaaa agaaccccca atttttgggg gcggaaaaac aaaactatgt
     2401 ttgcgctatg tgagtgtgct tcttgcattc atccctgtcg atgaacatcg acgaacataa
     2461 cacgatgtta aacaaaacaa aatattgttc acattccctg tgaccaaccg cgatcaggtc
     2521 tcctctcggt ggcgtgtgtt cgtgcatctt cctcgcgccg ccattcgtcc caggtacgat
     2581 tgaaacccag cgagcggaac agatgatccg gctgtttttc tggtgtgttg acgacagcaa
     2641 aaagcggtgc ctcacgggtt ttcagatgaa actccataag ttccggtgca ggtgatatgt
     2701 ggctgtctgc atcatgattt acggcaacac cataccctgc ataccgtaac cccttatcgg
     2761 tcagtgcact gataaccagc tggctgttat cggctgaggg aacggcaaac gcgggataca
     2821 gcgtaccatt aagccggaca acaccgccca gagagtcatc cacgcccatg accagcaaaa
     2881 gctgaagctg gcgggtttcc cggtcgacag aactcatgac cggcatcagc gtcggtggca
     2941 gacgtccctg cgtaaaatcc accttccttg ctgccagtga tggcatggct ggctggcggt
     3001 cttctccaag acagaaagac tccggccatg tcttcggctg gcggagattg cgggtatgtt
     3061 gcggccatgt ctggcaaacc tgcgtcagaa gttgctcaaa ggtcgcagag gaataaatac
     3121 gttgcagtgg tggatgttga ccgatttcgc ttcggtcaca gatataacca ctcctgtcac
     3181 gtattaaatc aacactctca aagatcctgg tgcggtattt ctccagctcg ttcccccaga
     3241 gcgtgtattc tccgttccgg ttgtgaagca gaaggtaaca agtcatttcc ccgttaccag
     3301 gcatgggagc ctcgccatac cccgtaacga ctgctctcag cacccctgaa tccataacgg
     3361 cattgtcatt tttcctgagc tgttccgctc gtcgctccgc gcgactacgt tctgtatcct
     3421 ccagctcctt ccggcgtaat tcatcttcac gtttaagcaa ctgggctctg agagctgcaa
     3481 ggccggattc cccccactgc tgccactgtt tttcaaatgc cgtctgactc gcgggaatgt
     3541 cctgtttctc caccttccgg taatgctgtc gcaatttttc catttgctgg ctcagagact
     3601 ggatttttcc ctgctcacta cggtattccg gtgcagccca ttgcatcagg ggaatacggg
     3661 aaaaaccgga cgaaaacggc gatgattttt tcaggctggc agcatggctc atcgcttcct
     3721 ttcgttcggt gttcagctct tcccagcgtc tgcgcgtcgc ctgcatatct gccatcatcg
     3781 acatggcgtt actggtgagt ttccatgccg cgttactgtc cttcggcaac gcttcgatga
     3841 tgtcacgtag tgtgtacgaa gttgcgttgt caggaagccc gatattcaga aggtcagcca
     3901 cacggcgggc aggctctgtc agcccgctgt tcctgagttc ggtgcgggaa atctgtattt
     3961 ccaggttaag cctgttaatc agacgattct gttcgccgcg ttctgtttcg ataccgcgtg
     4021 tttccatcgc acaggcagac tttccgaggt gaatacccgg cgttttctca agc
//
