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)
//