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OPENSEQ.org
RbcL-RbcS coevolution
Genes: A B A+B
Length: 472 111 570
Sequences: 645 453 150
Seq/Len: 1.37 4.08 0.26
MirrorTree (Pazo et al. 2001) 0.83
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.10 0.23
2 0.09 0.10 0.26
5 0.10 0.11 0.26
10 0.10 0.11 0.26
20 0.10 0.11 0.26
100 0.10 0.11 0.26
∞ 0.12 0.14 0.27
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
426_Q 25_Q 2.06 0.72 0.05
150_H 17_Y 1.67 0.49 0.02
317_L 88_R 1.53 0.40 0.01
142_V 88_R 1.41 0.33 0.01
458_L 92_F 1.38 0.31 0.01
179_A 17_Y 1.31 0.27 0.01
162_Y 25_Q 1.30 0.27 0.01
317_L 92_F 1.28 0.26 0.01
450_P 91_G 1.27 0.25 0.01
127_I 71_V 1.19 0.21 0.01
126_A 70_Q 1.16 0.20 0.00
179_A 39_H 1.15 0.20 0.00
342_F 68_P 1.14 0.20 0.00
285_G 17_Y 1.14 0.19 0.00
143_K 103_F 1.12 0.19 0.00
368_M 17_Y 1.08 0.17 0.00
61_G 13_E 1.07 0.17 0.00
262_I 68_P 1.07 0.17 0.00
115_T 25_Q 1.06 0.16 0.00
180_K 62_L 1.06 0.16 0.00
287_L 92_F 1.04 0.16 0.00
285_G 92_F 1.03 0.15 0.00
217_F 14_T 1.02 0.15 0.00
458_L 62_L 1.01 0.15 0.00
154_V 99_Q 1.01 0.15 0.00
384_M 60_L 1.01 0.15 0.00
197_T 60_L 1.01 0.15 0.00
139_V 89_V 1.01 0.15 0.00
369_P 14_T 1.00 0.14 0.00
449_S 91_G 1.00 0.14 0.00
210_R 17_Y 0.98 0.14 0.00
171_I 58_W 0.98 0.14 0.00
64_T 16_S 0.98 0.14 0.00
69_D 16_S 0.98 0.14 0.00
115_T 17_Y 0.98 0.14 0.00
370_G 17_Y 0.97 0.14 0.00
370_G 39_H 0.97 0.14 0.00
347_R 88_R 0.97 0.13 0.00
160_N 25_Q 0.97 0.13 0.00
460_K 34_I 0.96 0.13 0.00
203_I 50_P 0.96 0.13 0.00
225_S 57_M 0.95 0.13 0.00
369_P 25_Q 0.95 0.13 0.00
157_D 51_E 0.95 0.13 0.00
281_C 33_M 0.95 0.13 0.00
434_L 67_S 0.95 0.13 0.00
221_A 106_H 0.95 0.13 0.00
197_T 88_R 0.95 0.13 0.00
179_A 92_F 0.94 0.13 0.00
285_G 14_T 0.94 0.13 0.00
210_R 62_L 0.94 0.13 0.00
157_D 97_Q 0.94 0.13 0.00
311_L 97_Q 0.94 0.12 0.00
96_A 25_Q 0.94 0.12 0.00
197_T 58_W 0.93 0.12 0.00
180_K 81_E 0.93 0.12 0.00
180_K 58_W 0.93 0.12 0.00
220_D 58_W 0.93 0.12 0.00
371_V 14_T 0.92 0.12 0.00
127_I 68_P 0.92 0.12 0.00
219_A 91_G 0.92 0.12 0.00
318_S 106_H 0.91 0.12 0.00
307_H 70_Q 0.91 0.12 0.00
307_H 13_E 0.91 0.12 0.00
290_I 13_E 0.91 0.12 0.00
162_Y 14_T 0.91 0.12 0.00
171_I 60_L 0.90 0.12 0.00
210_R 14_T 0.90 0.12 0.00
451_E 91_G 0.90 0.12 0.00
83_H 38_F 0.90 0.12 0.00
61_G 49_N 0.89 0.11 0.00
307_H 62_L 0.89 0.11 0.00
78_K 25_Q 0.89 0.11 0.00
345_L 68_P 0.88 0.11 0.00
360_F 17_Y 0.88 0.11 0.00
369_P 92_F 0.88 0.11 0.00
286_V 17_Y 0.88 0.11 0.00
447_K 25_Q 0.87 0.11 0.00
158_L 99_Q 0.87 0.11 0.00
217_F 92_F 0.87 0.11 0.00
302_R 86_Y 0.87 0.11 0.00
226_Q 58_W 0.87 0.11 0.00
25_D 42_I 0.87 0.11 0.00
145_F 86_Y 0.87 0.11 0.00
397_L 21_L 0.86 0.10 0.00
210_R 94_N 0.86 0.10 0.00
370_G 92_F 0.86 0.10 0.00
157_D 99_Q 0.86 0.10 0.00
150_H 99_Q 0.86 0.10 0.00
81_C 71_V 0.86 0.10 0.00
94_Y 89_V 0.85 0.10 0.00
449_S 33_M 0.85 0.10 0.00
388_V 72_L 0.85 0.10 0.00
217_F 85_C 0.85 0.10 0.00
411_A 17_Y 0.85 0.10 0.00
220_D 82_Y 0.85 0.10 0.00
237_L 88_R 0.85 0.10 0.00
218_V 90_A 0.85 0.10 0.00
294_M 97_Q 0.84 0.10 0.00
154_V 25_Q 0.84 0.10 0.00
447_K 35_E 0.84 0.10 0.00
396_V 27_A 0.84 0.10 0.00
86_P 69_Q 0.84 0.10 0.00
412_P 38_F 0.84 0.10 0.00
348_E 84_D 0.84 0.10 0.00
48_D 20_P 0.84 0.10 0.00
96_A 85_C 0.84 0.10 0.00
38_R 92_F 0.83 0.10 0.00
235_H 83_G 0.83 0.10 0.00
458_L 88_R 0.83 0.10 0.00
140_A 17_Y 0.83 0.10 0.00
246_E 17_Y 0.83 0.10 0.00
40_S 34_I 0.83 0.10 0.00
301_Q 23_D 0.83 0.10 0.00
22_Y 62_L 0.82 0.10 0.00
217_F 39_H 0.82 0.10 0.00
301_Q 86_Y 0.82 0.10 0.00
369_P 17_Y 0.82 0.10 0.00
217_F 25_Q 0.82 0.10 0.00
41_P 16_S 0.82 0.10 0.00
285_G 39_H 0.82 0.10 0.00
311_L 51_E 0.82 0.10 0.00
78_K 17_Y 0.82 0.10 0.00
38_R 86_Y 0.82 0.10 0.00
25_D 82_Y 0.81 0.09 0.00
471_K 104_I 0.81 0.09 0.00
458_L 57_M 0.81 0.09 0.00
368_M 39_H 0.81 0.09 0.00
239_V 85_C 0.81 0.09 0.00
338_S 25_Q 0.81 0.09 0.00
325_S 10_R 0.81 0.09 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
10740 0.26 RbcL-RbcS coevolution Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.05 Done
4396 0.27 David1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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