E. Coli Genes

Donated on 7/13/2001

Data giving characteristics of each ORF (potential gene) in the E. coli genome. Sequence, homology (similarity to other genes) and structural information, and function (if known) are provided.

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Dataset Information

Additional Information

The data was collected from several sources, including GenProtEC (http://genprotec.mbl.edu/start) and SWISSPROT (http://www.expasy.ch/sprot/sprot-top.html). Structure prediction was made by PROF (http://www.aber.ac.uk/~phiwww/prof/index.html). Homology search was provided by PSI-BLAST (http://www.ncbi.nlm.nih.gov/BLAST/). The data is in Datalog format. Missing values are not explicit, but some genes have more relationships than others. E. coli genes (ORFs) are related to each other by the predicate ecoli_to_ecoli(EcoliNumber,E-value,Psi-blast_iteration). They are related to other (SWISSPROT) proteins by the predicate e_val(AccNo,E-value). All the data for a single gene (ORF) is enclosed between delimiters of the form: begin(model(EcoliNumber)). end(model(EcoliNumber)). The gene functional classes are in a hierarchy. See http://genprotec.mbl.edu/start (note: the classes may have changed since original data collection). There are two datalog files: ecoli_data.pl and ecoli_functions.pl 1. ecoli_functions.pl Lists classes and ORF functions. Lines are of the following form: class(5,1,1,'Colicin-related functions'). class(5,1,'Laterally acquirred elements'). class(5,'Extrachromosomal'). Arguments are up to 3 numbers (describing class at up to 3 different levels), followed by a string class description. For example: function(ecoli210,7,0,0,'b0217','putative aminopeptidase'). Arguments are ORF number, exactly 3 class numbers, gene name (or blattner number if no gene name), ORF description. 2. ecoli_data.pl Data for each ORF (gene) is delimited by begin(model(ecoliX)). end(model(ecoliX)). where X is the ORF number. Other predicates are as follows (examples): ecoli_orf(ecoliX). % X is ORF number ecoli_mol_wt(176624.1). % float ecoli_theo_pI(5.81). %float ecoli_atomic_comp(c,7940). % {c,h,n,o,s} , int ecoli_aliphatic_index(69.57). % float ecoli_hydro(-0.549). % float sec_struc(1,c,2). % int (start), {a,b,c}, int (length) sec_struc_coil(1,2). % int (start), int (length) sec_struc_beta(1,5). % int (start), int (length) sec_struc_alpha(1,7). % int (start), int (length) sequence_length(255). % int amino_acid_ratio(a,8.9). % amino_acid_char, float amino_acids(ecoli3013,a,70). % ORF_num, amino_acid_char, int amino_acid_pair_ratio(a,a,9.0). % amino_acid_char, amino_acid_char, float amino_acid_pairs(a,a,7). % amino_acid_char, amino_acid_char, int ecoli_to_ecoli(1170,1.0e-105,5). % ORF_num, double (e-value), int (iteration) e_val(o42893,2.0e-99). % accession_number, double (e-value) psi_iter(o42893,5). % accession_number, int (iteration) species(p52494,'candida_albicans__yeast_'). % accession_number, string mol_wt(p52494,104022). % accession_number, int classification(p52494,candida). % accession_number, name keyword(p25195,'plasmid'). % accession_number, string

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Ross King


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