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OPENSEQ.org
cIm_N_4_1_cyt1_2_human
Genes: A B A+B
Length: 347 325 548
Sequences: 8936 747 148
Seq/Len: 25.75 2.3 0.27
MirrorTree (Pazo et al. 2001) 0.29
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 0.03 0.02 0.00
2 0.03 0.02 0.00
5 0.03 0.02 0.00
10 0.03 0.02 0.00
20 0.04 0.02 0.00
100 0.04 0.02 0.02
∞ 0.04 0.02 0.22
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
297_I 308_R 1.78 0.57 0.00
136_L 277_A 1.31 0.28 0.00
291_Y 159_N 1.25 0.25 0.00
249_L 190_N 1.24 0.24 0.00
206_T 177_K 1.19 0.22 0.00
217_L 298_L 1.16 0.21 0.00
31_V 160_E 1.12 0.19 0.00
187_M 275_R 1.12 0.19 0.00
289_N 310_K 1.10 0.18 0.00
251_L 205_H 1.09 0.18 0.00
148_S 154_V 1.08 0.17 0.00
139_I 211_V 1.06 0.17 0.00
53_T 154_V 1.06 0.17 0.00
94_S 251_D 1.06 0.17 0.00
31_V 165_F 1.05 0.16 0.00
155_L 283_D 1.04 0.16 0.00
297_I 229_E 1.03 0.16 0.00
52_S 308_R 1.03 0.16 0.00
297_I 84_A 1.02 0.15 0.00
52_S 104_S 1.02 0.15 0.00
212_T 205_H 1.01 0.15 0.00
154_L 264_S 1.00 0.15 0.00
24_S 101_L 1.00 0.15 0.00
205_L 160_E 1.00 0.15 0.00
187_M 101_L 1.00 0.15 0.00
265_A 151_E 0.98 0.14 0.00
207_I 164_M 0.97 0.14 0.00
265_A 87_L 0.96 0.14 0.00
23_S 278_S 0.95 0.13 0.00
280_T 141_T 0.95 0.13 0.00
64_A 310_K 0.95 0.13 0.00
149_L 299_L 0.95 0.13 0.00
262_P 245_A 0.95 0.13 0.00
290_L 302_L 0.95 0.13 0.00
202_I 261_A 0.95 0.13 0.00
40_F 85_S 0.94 0.13 0.00
42_P 306_I 0.94 0.13 0.00
73_A 138_V 0.94 0.13 0.00
21_A 306_I 0.94 0.13 0.00
149_L 200_I 0.93 0.13 0.00
147_P 242_I 0.93 0.13 0.00
277_I 104_S 0.93 0.12 0.00
262_P 78_L 0.93 0.12 0.00
245_P 200_I 0.93 0.12 0.00
206_T 200_I 0.92 0.12 0.00
274_N 169_G 0.91 0.12 0.00
167_W 156_D 0.91 0.12 0.00
189_W 237_F 0.91 0.12 0.00
109_A 213_S 0.91 0.12 0.00
203_L 298_L 0.90 0.12 0.00
89_T 72_A 0.90 0.12 0.00
49_N 105_L 0.90 0.12 0.00
52_S 224_G 0.90 0.12 0.00
251_L 300_V 0.90 0.12 0.00
155_L 188_A 0.89 0.12 0.00
296_L 253_L 0.89 0.12 0.00
213_T 298_L 0.88 0.11 0.00
166_S 211_V 0.88 0.11 0.00
205_L 211_V 0.88 0.11 0.00
153_L 213_S 0.88 0.11 0.00
85_T 284_H 0.87 0.11 0.00
109_A 278_S 0.87 0.11 0.00
244_I 308_R 0.86 0.11 0.00
145_I 271_C 0.86 0.11 0.00
160_L 182_S 0.85 0.10 0.00
198_P 73_G 0.85 0.10 0.00
201_T 248_I 0.85 0.10 0.00
186_H 307_K 0.85 0.10 0.00
120_Q 202_R 0.85 0.10 0.00
281_I 151_E 0.85 0.10 0.00
143_Y 308_R 0.85 0.10 0.00
199_N 297_A 0.84 0.10 0.00
281_I 105_L 0.84 0.10 0.00
198_P 142_E 0.84 0.10 0.00
97_M 105_L 0.84 0.10 0.00
158_S 265_Q 0.83 0.10 0.00
254_L 148_L 0.83 0.10 0.00
231_S 72_A 0.83 0.10 0.00
169_G 139_C 0.82 0.10 0.00
252_G 282_H 0.82 0.10 0.00
141_I 287_R 0.82 0.10 0.00
41_I 169_G 0.82 0.10 0.00
51_R 245_A 0.82 0.10 0.00
158_S 94_Y 0.82 0.10 0.00
99_M 169_G 0.82 0.10 0.00
152_S 169_G 0.82 0.10 0.00
279_P 295_M 0.82 0.10 0.00
232_R 73_G 0.82 0.10 0.00
222_N 180_P 0.81 0.10 0.00
201_T 159_N 0.81 0.10 0.00
173_T 114_F 0.81 0.10 0.00
276_L 108_T 0.81 0.09 0.00
258_T 240_Q 0.81 0.09 0.00
166_S 212_F 0.80 0.09 0.00
297_I 129_F 0.80 0.09 0.00
247_T 313_V 0.80 0.09 0.00
109_A 240_Q 0.80 0.09 0.00
169_G 160_E 0.80 0.09 0.00
157_L 186_R 0.80 0.09 0.00
154_L 84_A 0.80 0.09 0.00
201_T 172_F 0.79 0.09 0.00
199_N 141_T 0.79 0.09 0.00
173_T 126_S 0.79 0.09 0.00
217_L 250_T 0.79 0.09 0.00
39_A 109_S 0.79 0.09 0.00
186_H 157_G 0.79 0.09 0.00
297_I 189_N 0.79 0.09 0.00
280_T 132_Y 0.79 0.09 0.00
141_I 145_A 0.79 0.09 0.00
189_W 314_L 0.79 0.09 0.00
262_P 69_A 0.79 0.09 0.00
154_L 255_F 0.79 0.09 0.00
51_R 192_A 0.78 0.09 0.00
228_L 221_P 0.78 0.09 0.00
159_I 151_E 0.78 0.09 0.00
288_L 309_H 0.78 0.09 0.00
99_M 255_F 0.78 0.09 0.00
78_N 225_V 0.78 0.09 0.00
36_N 114_F 0.78 0.09 0.00
158_S 199_Y 0.78 0.09 0.00
251_L 260_P 0.78 0.09 0.00
291_Y 107_H 0.78 0.09 0.00
186_H 243_A 0.77 0.09 0.00
262_P 213_S 0.77 0.09 0.00
179_L 277_A 0.77 0.09 0.00
98_I 277_A 0.77 0.09 0.00
24_S 193_L 0.77 0.09 0.00
136_L 69_A 0.77 0.09 0.00
91_N 267_A 0.77 0.09 0.00
155_L 208_E 0.77 0.09 0.00
40_F 169_G 0.77 0.09 0.00
289_N 101_L 0.77 0.09 0.00
31_V 159_N 0.77 0.09 0.00
209_I 188_A 0.77 0.09 0.00
9_I 186_R 0.76 0.09 0.00
139_I 281_E 0.76 0.09 0.00
73_A 137_G 0.76 0.09 0.00
212_T 266_I 0.76 0.09 0.00
194_L 260_P 0.76 0.09 0.00
31_V 130_V 0.76 0.08 0.00
130_L 202_R 0.76 0.08 0.00
262_P 97_S 0.76 0.08 0.00
73_A 271_C 0.76 0.08 0.00
187_M 183_E 0.76 0.08 0.00
132_T 312_S 0.76 0.08 0.00
25_H 132_Y 0.76 0.08 0.00
262_P 161_D 0.76 0.08 0.00
297_I 127_M 0.76 0.08 0.00
186_H 306_I 0.75 0.08 0.00
136_L 309_H 0.75 0.08 0.00
202_I 246_P 0.75 0.08 0.00
33_L 144_E 0.75 0.08 0.00
94_S 130_V 0.75 0.08 0.00
244_I 268_K 0.75 0.08 0.00
51_R 172_F 0.75 0.08 0.00
18_L 310_K 0.75 0.08 0.00
146_S 105_L 0.75 0.08 0.00
202_I 248_I 0.75 0.08 0.00
39_A 272_T 0.74 0.08 0.00
45_T 188_A 0.74 0.08 0.00
78_N 282_H 0.74 0.08 0.00
85_T 86_D 0.74 0.08 0.00
279_P 171_L 0.74 0.08 0.00
202_I 118_K 0.73 0.08 0.00
139_I 264_S 0.73 0.08 0.00
213_T 98_H 0.73 0.08 0.00
252_G 279_E 0.73 0.08 0.00
258_T 191_G 0.73 0.08 0.00
24_S 131_A 0.73 0.08 0.00
220_N 86_D 0.73 0.08 0.00
194_L 180_P 0.72 0.08 0.00
210_I 141_T 0.72 0.08 0.00
132_T 227_L 0.72 0.08 0.00
218_L 298_L 0.72 0.08 0.00
140_S 144_E 0.72 0.08 0.00
231_S 169_G 0.72 0.08 0.00
162_I 158_P 0.72 0.08 0.00
45_T 306_I 0.72 0.08 0.00
297_I 107_H 0.72 0.08 0.00
289_N 275_R 0.72 0.08 0.00
99_M 150_A 0.72 0.08 0.00
296_L 274_L 0.72 0.08 0.00
199_N 182_S 0.72 0.08 0.00
281_I 264_S 0.72 0.08 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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