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OPENSEQ.org
David1
Genes: A B A+B
Length: 472 111 574
Sequences: 605 623 153
Seq/Len: 1.28 5.61 0.27
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.04 0.23
2 0.00 0.05 0.27
5 0.00 0.09 0.27
10 0.00 0.10 0.27
20 0.01 0.11 0.26
100 0.01 0.12 0.26
∞ 0.03 0.17 0.28
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 1.71 0.53 0.00
142_V 88_R 1.61 0.46 0.00
317_L 88_R 1.60 0.45 0.00
150_H 17_Y 1.57 0.43 0.00
217_F 39_H 1.56 0.43 0.00
317_L 92_F 1.56 0.43 0.00
285_G 99_Q 1.52 0.40 0.00
268_T 99_Q 1.47 0.37 0.00
179_A 17_Y 1.33 0.29 0.00
150_H 99_Q 1.31 0.28 0.00
268_T 17_Y 1.29 0.27 0.00
369_P 99_Q 1.28 0.26 0.00
179_A 99_Q 1.22 0.23 0.00
179_A 92_F 1.21 0.23 0.00
126_A 70_Q 1.20 0.23 0.00
160_N 99_Q 1.20 0.23 0.00
368_M 17_Y 1.18 0.22 0.00
285_G 92_F 1.18 0.21 0.00
369_P 92_F 1.17 0.21 0.00
397_L 21_L 1.16 0.21 0.00
268_T 92_F 1.14 0.20 0.00
391_F 31_E 1.13 0.20 0.00
370_G 99_Q 1.13 0.20 0.00
447_K 25_Q 1.13 0.19 0.00
224_K 90_A 1.13 0.19 0.00
354_D 37_G 1.12 0.19 0.00
115_T 17_Y 1.12 0.19 0.00
180_K 62_L 1.12 0.19 0.00
127_I 71_V 1.11 0.18 0.00
210_R 17_Y 1.09 0.18 0.00
222_I 25_Q 1.08 0.17 0.00
347_R 88_R 1.07 0.17 0.00
162_Y 99_Q 1.07 0.17 0.00
221_A 62_L 1.07 0.17 0.00
281_C 33_M 1.06 0.17 0.00
78_K 99_Q 1.06 0.17 0.00
129_S 75_V 1.06 0.17 0.00
235_H 100_T 1.06 0.17 0.00
285_G 17_Y 1.05 0.16 0.00
210_R 94_N 1.05 0.16 0.00
411_A 99_Q 1.04 0.16 0.00
460_K 65_C 1.04 0.16 0.00
384_M 60_L 1.04 0.16 0.00
197_T 58_W 1.03 0.16 0.00
115_T 99_Q 1.03 0.16 0.00
154_V 92_F 1.02 0.15 0.00
38_R 86_Y 1.02 0.15 0.00
323_L 104_I 1.02 0.15 0.00
162_Y 25_Q 1.02 0.15 0.00
158_L 99_Q 1.01 0.15 0.00
370_G 39_H 1.01 0.15 0.00
466_F 91_G 1.00 0.15 0.00
179_A 39_H 1.00 0.15 0.00
307_H 62_L 0.99 0.14 0.00
171_I 58_W 0.98 0.14 0.00
220_D 87_I 0.98 0.14 0.00
179_A 88_R 0.98 0.14 0.00
115_T 25_Q 0.97 0.14 0.00
18_K 25_Q 0.97 0.14 0.00
451_E 72_L 0.97 0.14 0.00
307_H 93_D 0.97 0.14 0.00
347_R 62_L 0.97 0.14 0.00
10_Y 92_F 0.97 0.14 0.00
61_G 13_E 0.97 0.14 0.00
217_F 14_T 0.96 0.14 0.00
126_A 68_P 0.96 0.14 0.00
140_A 17_Y 0.96 0.13 0.00
34_L 62_L 0.96 0.13 0.00
323_L 89_V 0.95 0.13 0.00
107_E 25_Q 0.95 0.13 0.00
286_V 17_Y 0.95 0.13 0.00
157_D 51_E 0.95 0.13 0.00
393_D 104_I 0.95 0.13 0.00
301_Q 86_Y 0.94 0.13 0.00
217_F 25_Q 0.94 0.13 0.00
78_K 17_Y 0.94 0.13 0.00
302_R 86_Y 0.94 0.13 0.00
145_F 86_Y 0.94 0.13 0.00
110_V 24_R 0.94 0.13 0.00
369_P 14_T 0.94 0.13 0.00
210_R 99_Q 0.93 0.13 0.00
458_L 92_F 0.93 0.13 0.00
423_A 93_D 0.93 0.12 0.00
221_A 91_G 0.93 0.12 0.00
268_T 25_Q 0.92 0.12 0.00
360_F 17_Y 0.92 0.12 0.00
179_A 98_C 0.92 0.12 0.00
221_A 75_V 0.92 0.12 0.00
353_A 92_F 0.92 0.12 0.00
39_F 62_L 0.92 0.12 0.00
458_L 85_C 0.92 0.12 0.00
127_I 68_P 0.92 0.12 0.00
370_G 92_F 0.91 0.12 0.00
449_S 91_G 0.91 0.12 0.00
449_S 99_Q 0.91 0.12 0.00
139_V 89_V 0.91 0.12 0.00
34_L 98_C 0.91 0.12 0.00
311_L 97_Q 0.90 0.12 0.00
33_L 31_E 0.90 0.12 0.00
434_L 67_S 0.90 0.12 0.00
354_D 82_Y 0.90 0.12 0.00
283_D 75_V 0.90 0.12 0.00
197_T 88_R 0.90 0.12 0.00
296_A 75_V 0.90 0.12 0.00
157_D 97_Q 0.89 0.12 0.00
220_D 58_W 0.89 0.12 0.00
242_P 76_R 0.89 0.11 0.00
425_V 98_C 0.89 0.11 0.00
47_A 86_Y 0.89 0.11 0.00
6_S 62_L 0.89 0.11 0.00
354_D 81_E 0.89 0.11 0.00
41_P 16_S 0.89 0.11 0.00
287_L 92_F 0.89 0.11 0.00
64_T 16_S 0.88 0.11 0.00
69_D 16_S 0.88 0.11 0.00
10_Y 99_Q 0.88 0.11 0.00
128_R 20_P 0.88 0.11 0.00
81_C 71_V 0.87 0.11 0.00
203_I 50_P 0.87 0.11 0.00
85_E 33_M 0.87 0.11 0.00
359_V 41_L 0.87 0.11 0.00
107_E 98_C 0.86 0.11 0.00
453_A 91_G 0.86 0.11 0.00
129_S 34_I 0.86 0.11 0.00
75_D 88_R 0.86 0.11 0.00
348_E 93_D 0.86 0.11 0.00
224_K 91_G 0.86 0.11 0.00
336_K 47_H 0.86 0.11 0.00
317_L 72_L 0.85 0.10 0.00
284_N 32_Y 0.85 0.10 0.00
318_S 11_R 0.85 0.10 0.00
283_D 72_L 0.85 0.10 0.00
411_A 88_R 0.84 0.10 0.00
140_A 92_F 0.84 0.10 0.00
154_V 17_Y 0.84 0.10 0.00
48_D 30_I 0.84 0.10 0.00
75_D 75_V 0.84 0.10 0.00
213_D 100_T 0.84 0.10 0.00
86_P 104_I 0.84 0.10 0.00
369_P 17_Y 0.84 0.10 0.00
154_V 100_T 0.84 0.10 0.00
180_K 82_Y 0.84 0.10 0.00
217_F 85_C 0.83 0.10 0.00
210_R 62_L 0.83 0.10 0.00
285_G 14_T 0.83 0.10 0.00
28_P 85_C 0.83 0.10 0.00
82_Y 81_E 0.82 0.10 0.00
465_E 82_Y 0.82 0.10 0.00
78_K 92_F 0.82 0.10 0.00
61_G 49_N 0.82 0.10 0.00
301_Q 46_E 0.81 0.10 0.00
242_P 56_T 0.81 0.10 0.00
391_F 77_E 0.81 0.10 0.00
271_F 36_Q 0.81 0.10 0.00
368_M 21_L 0.81 0.09 0.00
210_R 53_F 0.80 0.09 0.00
368_M 88_R 0.80 0.09 0.00
137_F 33_M 0.80 0.09 0.00
203_I 86_Y 0.80 0.09 0.00
79_G 52_E 0.80 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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