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This page describes an analysis of the thermophilic and mesophilic genomes that tried to identify protein structural features which lead to thermal stability of proteins in thermophiles. We found that salt bridge interaction is more prevalent in thermophilic proteins than in their mesophilic counterparts and it can play an important role in proteins thermotability. We also studied the effect of other factors such as protein length and deamidaion.
| Table name | Links | Fields | Description |
| Organisms |
data, head |
Organism, Genome id, No of proteins, Physiological condition | This table lists all the organisms that are included in calculation |
|
Raw Sequences [Seq.fa] |
AA,AF, MJ, MT, OT, EC, HI, HP, MG, MP, SC, SS | AA, AF, MJ, MT, OT, EC, HI, HP, MG, MP, SC, SS | Contains sequence file for 11 genomes |
|
Secondary Structure [Gorss.fa] |
AA,AF, MJ, MT, OT, EC, HI, HP, MG, MP, SC, SS | AA, AF, MJ, MT, OT, EC, HI, HP, MG, MP, SC, SS | Contains predicted secondary structure sequence file for 11 genomes |
| amino acid composition in entire genome | data | Thermophiles, mesophiles, AA, AF, MJ, MT, OT, EC, HI, HP, MG, MP, SC, SS, A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T V, W, Y | Amino acid composition |
| amino acid composition in helix |
data, head |
Thermophiles, mesophiles, AA, AF, MJ, MT, OT, EC, HI, HP, MG, MP, SC, SS, A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T V, W, Y | Amino acid composition |
| Plot of helix amino acid composition | plot | Total content of any amino acid is summed upto 100% | Plot shows that K,R and E,D content in helix increases from mesophilic to thermophilic genomes |
| Comprehensive LOD value table for helix(data1) and genome (data2) |
aa, sep AA, AF, MJ, MT, OT, EC, HI, HP, MG, SC, SS, A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T V, W, Y |
Tables includes amino acid composition, raw counts and expected counts, odd values and lod values for all 400 pairs at different spacing | |
| LOD values of saltbridge pairs | data | Spacing, pair, AA, AF, MJ, MT, OT, EC, HI, HP, MG, SC, SS | Table contains LOD values for EK, ER, DR at spacing of 3 and 4 for helix and g enome. |
| LOD values of saltbridge pairs | data | Spacing, pair, AA, AF, MJ, MT, OT, EC, HI, HP, MG, SC, SS | Table contains LOD values for EK, ER, DR at spacing of 3 and 4 for helix and genome. |
| Diagram showing LOD values for EK(3) and Ek(4) | plot | - | - |
| Rank statistics of salt bridge pairs |
data, head |
SEP, PAIR, AA, AF, MJ, MT, OT, EC, HI, HP, MG, SC, SS | Table lists only those ranks which appear within first 20. ( both for helix and genome) |
| List of 52 COGs | data | COGcat, COGid, COGrib_pro, COGtrna_syn, COGother | Table lists 52 COGs selected for this study |
| List of COG proteins having PDB structure |
data, head |
cogid, class, cat, pthermophileid (pdbid for correspondong cog sequencs) | "cat" means category. This of COG proteins found in all of the eleven genomes. "class" defines the functional classification as described by NCBI. |
| Statistics for COG salt-bridges |
data, head |
cat, pdbid, arc_avg, mes_avg, arc-mes ( means difference between arc_avg and mes_avg) |
arc_avg and mes_avg are the average number of salt-bridge counts in archaeal cog and mesophilic cog respectively |
| Length data of all eleven genomes |
data, head |
binnam_, ibin, AA, AF, MJ, MT, OT, EC, HI, HP, MG, SC, SS | Table contains the distrbution of protein at different length |
| Plot of length distribution | plot | %frequency, protein length | Distribution of length data for all 11 genomes, |
| Plot of length distribution in terms of percentage composition | plot | protein content, length | Distribution of length composition data for all 11 genomes, |
| Distribution of random LOD values | plot | - | Plot of EK(3) LOD values for randomly generated thermophilic and mesophilic genomes |
| Plot of fit curves for length distribution | plot | - | Plot of fit curve with length distribution data of overall genome sequences and that of 52 COG sequences for all genomes |
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