Help : pathway with protein structures
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- EC Number
- Enzyme Commission number (http://www.chem.qmul.ac.uk/iubmb/enzyme/).
- Locus tag
- Locus tag is the unique identifier for a gene in each genome. These ID numbers are used by the international sequence collaboration (DDBJ/EMBL/GenBank). Examples are listed below with its organism name.
- TTHA1234, TTHB123, TTHC123; Thermus thermophilus HB8
- TM1234; Thermotoga maritima MSB8
- GK1234; Geobacillus kaustophilus HTA426
- Syto1234; Symbiobacterium toebii
- JW1234; Escherichia coli K-12
- APE1234; Aeropyrum pernix K1
- PH1234; Pyrococcus horikoshii OT3
- ST1234; Sulfolobus tokodaii strain7
- aq_1234; Aquifex aeolicus VF5
- BLAST Hit PDB
- PDB ID code for which amino acid sequence has a significant homology to the query sequence using NCBI BLAST sequence analysis (blastp).
- Hit evalue
- BLAST e-value of the best hit. "Blank" means that the e-value is less than 0.001 and there is no significant hit of its query sequence.
- Match Index
- (identity * overlap) / (query_length)^2, which is a matching index between a query and its best hit of BLAST analysis. When Match Index equal to 1.00 (i.e. BLAST e-value equal to 0.0), the structure of the query itself has been determined.
- "OK" indicates that the structure of Thermus thermophilus protein has already been solved, and "HOM" indicates that the structure of the homologous protein not from Thermus thermophilus has been solved.
The template pathway is originally generated by KEGG (http://www.genome.jp/kegg/). An open reading frame is colored differently. Green color means that an open reading frame from Thermus thermophilus is assigned into the protein in the pathway. Pink color means that the structure of homologous protein not from Thermus thermophilus has been solved, whereas red color means that the structure of Thermus thermophilus protein has been solved.
Last modified: Mon May 01 15:04:59 JST 2006