LOCUS       NZ_CP008717             4237 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli strain ST648 isolate Pleural Effusion of Patients
            with Empyema Thoracis plasmid pEC648_3, complete sequence.
ACCESSION   NZ_CP008717
VERSION     NZ_CP008717.1
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 4237)
  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  JOURNAL   Unpublished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 4237)
  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
            CP008717.1.
            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..4237
                     /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_3"
                     /geo_loc_name="China:Beijing"
                     /lat_lon="39.93 N 116.35 E"
                     /collection_date="2009-05-24"
                     /collected_by="Dezhi Li"
     gene            749..1264
                     /locus_tag="FH07_RS25690"
                     /old_locus_tag="FH07_00720"
     CDS             749..1264
                     /locus_tag="FH07_RS25690"
                     /old_locus_tag="FH07_00720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_060684538.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAIQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1445..1735
                     /locus_tag="FH07_RS28715"
     CDS             1445..1735
                     /locus_tag="FH07_RS28715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000160396.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_024241218.1"
                     /translation="MTKHDAIRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHF
                     RNSTPNTVASQLLNARVKLGCASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="transcriptional regulator"
     gene            1823..2086
                     /locus_tag="FH07_RS25695"
                     /old_locus_tag="FH07_00725"
     CDS             1823..2086
                     /locus_tag="FH07_RS25695"
                     /old_locus_tag="FH07_00725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            2091..3089
                     /locus_tag="FH07_RS25700"
                     /old_locus_tag="FH07_00730"
     CDS             2091..3089
                     /locus_tag="FH07_RS25700"
                     /old_locus_tag="FH07_00730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            3086..3799
                     /locus_tag="FH07_RS25705"
                     /old_locus_tag="FH07_00735"
     CDS             3086..3799
                     /locus_tag="FH07_RS25705"
                     /old_locus_tag="FH07_00735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     Typing          2092..2894
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 ctgcattgct cttttgccga cctcaaaacc cctagcgtgt ttttgtttcc cgatctctag
       61 aaccaccgag ccgccacggt tccggcagcg ccttgagcgc aaccggaaac cgtctgggga
      121 gaaccccaga cccccatcgc tgtaacatcg acggtctacg accacctacc aaccgtgtgg
      181 ctacctgttc catgctaatg ggctttgcag ggggctggcg cggttcctgg cgacctgaaa
      241 gcccctggtt aggggtatcg gcgcgcctga cctcctgaaa ccctctgtaa gcatttttcg
      301 cgcctttcat gccctgacgg gcatctaaag cccgtttcgt gcgtctgagc gcgttttaag
      361 agctaagacg actaaaacat taccaacacc tgaaaatcgc gttctggtgc tctggatggc
      421 ccacagaacg cattttcgaa cagaacagca acggcatttc tgacaacatg cgagaggtga
      481 tcccgctcgc cgcagcccca gcgaccgaac gtagtgagcg agtgggcgag gaagcggaag
      541 agaattgata gccataattg agcacctacg ctccttagtt aagaactaag aagggaaatt
      601 ctcggaaccc gcatgaatcc tagaaagtgg tgatcaggat ctgtaccttg taagctcaga
      661 tccggtacct tgcaggctca aaaattgctt gattttgagc ttatgaggat ttattgtgaa
      721 tctccaaagc ccaaaaaagg atgcaataat gagctcgcta agcttacaga gatacgaaac
      781 aaacccgttt ttagagctta tgacgatccc gatgaaaggg aaacggatac aagtatctcg
      841 tcttgggcgg gatgacaatg ttttggttaa tcaaaacacg ggagaaaagt ttggaacaca
      901 tgtaaccact tttaagcgtg tagatagtga gcaatttgtt aagttgttta ctgcgaatat
      961 tgggttaacg tttgatttat catcggcagg aattaaagct tttaatgttc ttttatgggc
     1021 tattcaaaaa caagcctttg caaaggatca ggttcttttg gattcaaggg ctcttgatga
     1081 ctttttaaaa agctatgata gcttaaaact tagttatgct acgttaaaga gaggaattaa
     1141 cgagttagaa aaagctcaga ttatagcaaa gacaatgcgt aaaggatttt attttataaa
     1201 ccccaatttt gtatttaatg gagatcgaat agcatttaca accctaattg agagggattg
     1261 ttaatcgata gaacaataca atgcaggata gacaatccac tagaaattgc atgcaatttt
     1321 cagtggattg tccaaaaacg atgtttttgc ctgtgcctgc cgcaggctac tagaagtagt
     1381 cgcaggcgaa caaaagtggt gttttgttcg cctgctaatc acaacaacct ggctagaggt
     1441 ttttatgact aaacatgatg ctatacgcat ttctcaactt catcaaattt tttacgatga
     1501 tgatggatta attgattcag aaaagaacgt gactatttta tacagtatag gatttacagt
     1561 tgatgaaata gctcatttta gaaattcaac accaaacaca gttgcgagtc agctattaaa
     1621 tgcaagggtt aaattaggtt gcgcctcggt ttcatcttta aagccaatga tcttattaag
     1681 attgcttttg aacataaaag agattcgttt tggattcgaa actgattgca aataatatag
     1741 ttcaataggt atttttgctc ttgactagaa ttacaattgc tgattgtatc agcaattgta
     1801 atgtccatac gaggaatcaa agatgaaaaa aatttgtacg ctcttaatgt ctattttcat
     1861 tctttccgca tgtggtgaag atacaaaatc atcagattgg tggcttaatc atcccaaaga
     1921 agcgacggag aaatataagg agtgtaaaaa gtcaggggaa gattctgtta attgtcaaaa
     1981 tgttaaaaaa gttgccggaa ttattggtag aacctatggc cctatgcttg aaatacttaa
     2041 ggctgagtca gctgaatatg ataagcaaca tggattgaac aggtgataac atgtctggtt
     2101 tctttgaaaa gtttaatagc gaagttgtta gtaaaatcga agagatgacc aaaccacttc
     2161 aaagtcaatt aggtcaggat atgttatctc ttctaagtgc aggtattagc gtttatatcc
     2221 tctgggttgg ctatcaaata ttggcaggga aacgccagac cccattacaa gatctcgtct
     2281 gggatctatc aaaatttgcc attattttaa cattcgtaag caatgctgat ggctatctga
     2341 cggcagcaat ggatgctatt aaatctatga aggatgggtt ccttggtaaa cctgtatggg
     2401 caacgctaga taccatgtgg agtacaactc agcttttggc tgacaaagtt tatgctatgg
     2461 atcaatccaa atatgtgtca gttgaaggtg gaatcgggtc aatgttggtt tggggaggaa
     2521 gtatcctgat tatgtctgta gcggctgtta tttacatgct tgccgatgta acaatgcagt
     2581 tagctattct tgtagctccg atatttatcg gttgttatat gtttggattc actagagtaa
     2641 tgtttaataa ctggcttggt atattatttt ctagtgtatt tactgttatt tttgctggag
     2701 ttctcgtcaa aattggtacc gagtttcaaa ctgatatgct tagtcagata tcgagagatg
     2761 ctaactcaac aaatatttta acaatgggcg caatggcatt tgtaattgga gttctgattg
     2821 ctgtctttgt ctggaaatca tcgagtttcg cgcagcagct tgccggtgca ggtgttgaag
     2881 gtactcttca gggaatggct cttttaggga ttggggctgc tggaatggcc gtagagaaaa
     2941 cgagaaacca gatgaaacgt ggaacgcgaa cagccgccga atgggcaggt gaaaaagggg
     3001 agcagaaacg ggcttcaata ggcgcattgg gaatggaagc aagaagacga gcatccctgg
     3061 aaaaagcacg tgcgaggaat tcagcatgaa caaaaaacta attttttcag tacttttgtg
     3121 cttattttca tttggttctg tcgcaggtat tccggttgct attgatgcca gtccggaatg
     3181 ggctgttgaa gccacaagat ggacagaacg actcaaacaa tggtctgaaa cagcgcggca
     3241 ttatcaaagt cagattcagg catataaaga ccagttagcc acggcaacag gtataaggaa
     3301 tattgcggca ttcacaaatg aactaagtaa cctacaatca gagctggcaa acatttataa
     3361 gcaggggaac agttatattt ctgattttac cagtaatcct gaaggtgcat taagtagtca
     3421 ggcgaaaaat ctgttcagca agtatggtgc ttttaatatg tgttctacag gcattgaaag
     3481 ttctgataac ctttgtaagg ccagaatagt ttcaacggcc gctagcattg aacagggaaa
     3541 tgagataaat aagcagctat caagtgcaat gtctcagatt cagagtttaa gtaaccgaat
     3601 tgagtcttca aaggatatga aagaatccca ggatttggct aacgcattgc aggcgcagtc
     3661 gttaaaaata caggcaatta aaatgcagta tgatgtatgg gatagtaaaa acagggctga
     3721 tgcggaaatg ttgaaagagc aaaagtatgc tgagtatcgc ctgcgtcaga aaaatgcaaa
     3781 gataccgagt ttcgaatgat atgataaagc taaataagct aaaagaatgg gtagataatc
     3841 attggtctag attgaatagt accggttcta caccgccgcc actgttaatc tcgctaccaa
     3901 tcatagttat tgttttaagt gtggagctta cgttaaagct gattaatgct ttaatgtatt
     3961 atggtacatt gcaatttatc actgataaaa ttgaaaagag gtttgttccc agcggtggta
     4021 taaaagaaag actccttttt acgttaaagc tgttttgtat tttacttctg ttattaatag
     4081 taatgcgatt ttcaatgaag taaaaaataa aggtcatcga atagatggcc ttttctattc
     4141 taaattctaa atatagagcc tgcggcaggc acaggcaaaa acatcgtttt tggacaatct
     4201 gattcaaatg ttaacatttg acatcggatt gtctatc
//
