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Escherichia coli strain MOD1-EC5206 MOD1-EC5206_84_length_6521_cov_63.9708, whole genome shotgun sequence

NCBI Reference Sequence: NZ_NLQU01000084.1

FASTA Graphics 

LOCUS       NZ_NLQU01000084         6521 bp    DNA     linear   CON 13-JUN-2024
DEFINITION  Escherichia coli strain MOD1-EC5206
            MOD1-EC5206_84_length_6521_cov_63.9708, whole genome shotgun
            sequence.
ACCESSION   NZ_NLQU01000084 NZ_NLQU01000000
VERSION     NZ_NLQU01000084.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04448475
            Assembly: GCF_002231565.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6521)
  AUTHORS   Gangiredla,J., Mammel,M.K., Barnaba,T.J., Tartera,C., Gebru,S.T.,
            Patel,I.R., Leonard,S.R., Kotewicz,M.L., Lampel,K.A., Elkins,C.A.
            and Lacher,D.W.
  TITLE     Species-Wide Collection of Escherichia coli Isolates for
            Examination of Genomic Diversity
  JOURNAL   Genome Announc 5 (50), e01321-17 (2017)
   PUBMED   29242221
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6521)
  AUTHORS   Gangiredla,J., Barnaba,T., Gebru,S., Mammel,M.K., Lacher,D.,
            Tartera,C., Patel,I.R., Leonard,S., Lampel,K.A. and Elkins,C.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUL-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            NLQU01000084.1.
            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/
            
            ##Genome-Assembly-Data-START##
            Assembly Method        :: SPAdes v. 3.8.2
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 62.8x
            Sequencing Technology  :: Illumina NextSeq 500
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002231565.1-RS_2024_06_13
            Annotation Date                   :: 06/13/2024 04:47:59
            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)                     :: 5,187
            CDSs (total)                      :: 5,094
            Genes (coding)                    :: 4,833
            CDSs (with protein)               :: 4,833
            Genes (RNA)                       :: 93
            rRNAs                             :: 7, 3, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 6 (5S)
            partial rRNAs                     :: 1, 3, 3 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 261
            CDSs (without protein)            :: 261
            Pseudo Genes (ambiguous residues) :: 0 of 261
            Pseudo Genes (frameshifted)       :: 78 of 261
            Pseudo Genes (incomplete)         :: 191 of 261
            Pseudo Genes (internal stop)      :: 44 of 261
            Pseudo Genes (multiple problems)  :: 47 of 261
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..6521
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /submitter_seqid="MOD1-EC5206_84_length_6521_cov_63.9708"
                     /strain="MOD1-EC5206"
                     /isolation_source="large intestine white-tailed deer
                     (Odocoileus virginianus)"
                     /host="Odocoileus virginianus"
                     /db_xref="taxon:562"
                     /geo_loc_name="USA: PA"
                     /collection_date="1975-01-01"
                     /collected_by="Pennsylvania State University | Escherichia
                     coli Reference Center"
     gene            <1..849
                     /locus_tag="AXA35_RS25895"
     CDS             <1..849
                     /locus_tag="AXA35_RS25895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_708765.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="autotransporter domain-containing protein"
                     /protein_id="WP_089570679.1"
                     /translation="NGGIARGATPESSGSYGFVRLEGDLLRTEVAGMSVTAGVYGAAG
                     HSSVDVKDDDGSRAGTVRDDAGSLGGYLNLTHTSSGLWADIVAQGTRHSMKASSDNND
                     FRARGWGWLGSLETGLPFSITDNLMLEPQLQYTWQGLSLDDGQDNAGYVKFGHGSAQH
                     VRAGFRLGSHNDMNFGKGTSSRDTLRGSAKHSVRELPVNWWVQPSVIRTFSSRGDMSM
                     GTAAAGSNMTFSPSQNGTSLDLQAGLEARVRENITLGVQAGYVHSVSGSSAEGYNGQA
                     TLNVTF"
     gene            970..3486
                     /locus_tag="AXA35_RS25900"
     CDS             970..3486
                     /locus_tag="AXA35_RS25900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_708766.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001348608.1"
                     /translation="MLQIVGALILLIAGFAILRLLFRALISTASALAGLILLCLFGPA
                     LLAGYITERITRLFHIRWLAGVFLTIAGMIISFMWGLDGKHIALEAHTFDSVKFILTT
                     ALAGGLLAVPLQIKNIQQNGITPEDISKEINGYYCCFYTAFFLMACSACAPLIALQYD
                     ISPSLMWWGGLLYWLAALVTLLWAASQIQALKKLTCAISQTLEEQPVLNSKSWLTSLQ
                     NDYSLPDSLTERIWLTLISQRISRGELREFELADGNWLLNNAWYERNMAGFNEQLKEN
                     LSFTPDELKTLFRNRLNLSPEANDDFLDRCLDGGDWYPFSEGRRFVSFHHVDELRICA
                     SCGLTEVHHAPENHKPDPEWYCSSLCRETETLCQEIYERPYNSFISDATANGLILMKL
                     PETWSTNEKMFASGGQGHGFAAERGNHIVDRVRLKNARILGDNNARNGADRLVSGTEI
                     QTKYCSTAARSVGAAFDGQNGQYRYMGNNGPMQLEVPRDQYAGAVETMRNKIREGKVP
                     GVTDPAEASRLIRRGHLTYTQARNITRFGTIESVTYDIAEGSVVSLAAGGISFALTAS
                     VFWLSTGDRDAALQTAAVQAGKTFTRTLAVYVTTQQLHRLSVVQGMLKHIDFSTASPT
                     VRLALQKGTGAGNISALNKVMKGTLVTSLALVAVTTGPDMIKMLRGRISGAQFIRNLA
                     VASSGVAGGAVGSVAGGILFSPLGPFGALTGRVVGGVLGGMIASAVSGKIAGALVEED
                     RVKILAMIQEQVTWLAGSFLLTGHEIENLNENLARVIDQNALEIIFAAGIQQRAATNM
                     LIKPLVVSIIRQRPVMEYDASHLGNMVNRLEEALPPELPA"
     gene            3562..4017
                     /locus_tag="AXA35_RS25905"
     CDS             3562..4017
                     /locus_tag="AXA35_RS25905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_708767.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IrmA family protein"
                     /protein_id="WP_000581504.1"
                     /translation="MIHLFKTCMITAFILGLTWSAPLRAQDQRYISIRNTDTIWLPGN
                     ICAYQFRLDNGGNDEGFGPLTITLQLKDKYGQTLVTRKMETEAFGDSNATRTTDAFLE
                     TECVENVATTEIIKATEESNGHRVSLPLSVFNPQDYHPLLITVSGKNVN"
     gene            complement(4130..5701)
                     /locus_tag="AXA35_RS25910"
     CDS             complement(4130..5701)
                     /locus_tag="AXA35_RS25910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012904571.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS66-like element ISCro1 family transposase"
                     /protein_id="WP_000381395.1"
                     /translation="MDTSLAHENARLRALLQTQQDTIRQMAEYNRLLSQRVAAYASEI
                     NRLKALVAKLQRMQFGKSSEKLRAKTERQIQEAQERISALQEEMAETLGEQYDPVLPS
                     ALRQSSARKPLPASLPRETRVIRPEEECCPACGGELSSLGCDVSEQLELISSAFKVIE
                     TQRPKQACCRCDHIVQAPVPSKPIARSYAGAGLLAHVVTGKYADHLPLYRQSEIYRRQ
                     GVELSRATLGRWTGAVAELLEPLYDVLRQYVLMPGKVHADDIPVPVQEPGSGKTRTAR
                     LWVYVRDDRNAGSQMPPAVWFAYSPDRKGIHPQNHLAGYSGVLQADAYGGYRALYESG
                     RITEAACMAHARRKIHDVHARAPTYITTEALQRIGELYAIEAEVRGCSAEQRLAARKA
                     RAAPLMQSLYDWIQQQMKTLSRHSDTAKAFAYLLKQWDALNVYCSNGWVEIDNNIAEN
                     ALRGVAVGRKNWMFAGSDSGGEHAAVLYSLIGTCRLNNVEPEKWLRYVIEHIQDWPAN
                     RVRDLLPWKVDLSSQ"
     gene            complement(5721..6068)
                     /gene="tnpB"
                     /locus_tag="AXA35_RS25915"
     CDS             complement(5721..6068)
                     /gene="tnpB"
                     /locus_tag="AXA35_RS25915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_858152.1"
                     /note="TnpB, as the term is used for proteins encoded by
                     IS66 family insertion elements, is considered an accessory
                     protein, since TnpC, encoded by a neighboring gene, is a
                     DDE family transposase; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS66 family insertion sequence element accessory
                     protein TnpB"
                     /protein_id="WP_000624622.1"
                     /translation="MISLPAGSRIWLVAGITDMRNGFNGLASKVQNVLKDDPFSGHLF
                     IFRGRRGDQIKVLWADSDGLCLFTKRLERGRFVWPVTRDGKVHLTPAQLSMLLEGINW
                     KHPKRTERAGIRI"
     gene            complement(6068..>6445)
                     /gene="tnpA"
                     /locus_tag="AXA35_RS25920"
                     /pseudo
     CDS             complement(6068..>6445)
                     /gene="tnpA"
                     /locus_tag="AXA35_RS25920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001743492.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence
                     IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="IS66-like element accessory protein TnpA"
CONTIG      join(NLQU01000084.1:1..6521)
//
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