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OPENSEQ.org
1GP2
Genes: A B A+B
Length: 353 340 649
Sequences: 1684 28386 314
Seq/Len: 4.77 83.49 0.48
MirrorTree (Pazo et al. 2001) 0.32
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 0.08 0.06 0.07
2 0.09 0.08 0.11
5 0.09 0.10 0.20
10 0.09 0.13 0.29
20 0.10 0.16 0.45
100 0.12 0.28 1.00
∞ 0.15 0.31 1.35
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
13_E 294_C 1.29 0.39 0.00
72_V 299_A 1.11 0.27 0.00
48_I 79_L 1.09 0.26 0.00
318_I 216_G 1.08 0.26 0.00
285_C 315_V 1.07 0.25 0.00
272_L 193_A 1.07 0.25 0.00
20_R 70_L 1.06 0.24 0.00
327_D 146_L 1.05 0.24 0.00
305_Q 82_W 0.99 0.21 0.00
93_D 203_A 0.99 0.20 0.00
158_L 315_V 0.99 0.20 0.00
215_E 187_V 0.95 0.18 0.00
163_Q 61_M 0.94 0.18 0.00
289_Y 312_D 0.91 0.17 0.00
296_E 103_C 0.90 0.16 0.00
164_P 273_I 0.90 0.16 0.00
154_Y 229_I 0.89 0.16 0.00
277_I 155_N 0.89 0.16 0.00
121_E 113_A 0.89 0.16 0.00
227_S 114_C 0.89 0.16 0.00
287_P 103_C 0.88 0.16 0.00
221_I 160_S 0.88 0.15 0.00
91_K 329_T 0.88 0.15 0.00
83_I 64_G 0.88 0.15 0.00
30_A 158_V 0.88 0.15 0.00
298_A 250_C 0.87 0.15 0.00
156_N 149_C 0.87 0.15 0.00
59_G 201_S 0.86 0.15 0.00
72_V 244_G 0.86 0.15 0.00
76_T 284_L 0.85 0.15 0.00
264_I 319_G 0.85 0.14 0.00
22_L 320_V 0.85 0.14 0.00
231_L 327_V 0.84 0.14 0.00
28_K 254_D 0.84 0.14 0.00
221_I 214_R 0.84 0.14 0.00
83_I 224_G 0.84 0.14 0.00
301_Y 79_L 0.83 0.14 0.00
14_R 202_G 0.83 0.14 0.00
226_L 244_G 0.83 0.14 0.00
139_F 81_I 0.82 0.13 0.00
64_E 336_L 0.82 0.13 0.00
53_K 139_L 0.82 0.13 0.00
76_T 129_R 0.82 0.13 0.00
289_Y 327_V 0.81 0.13 0.00
212_H 264_Y 0.81 0.13 0.00
16_K 79_L 0.81 0.13 0.00
226_L 74_S 0.81 0.13 0.00
226_L 278_F 0.80 0.13 0.00
23_R 193_A 0.80 0.13 0.00
69_K 190_L 0.80 0.13 0.00
53_K 180_F 0.80 0.13 0.00
85_R 100_V 0.80 0.13 0.00
191_K 201_S 0.78 0.12 0.00
352_L 87_T 0.78 0.12 0.00
63_E 199_F 0.78 0.12 0.00
302_I 245_S 0.78 0.12 0.00
272_L 79_L 0.78 0.12 0.00
175_R 170_D 0.78 0.12 0.00
135_V 79_L 0.77 0.12 0.00
252_I 134_R 0.77 0.12 0.00
20_R 102_T 0.77 0.12 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)
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