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OPENSEQ.org
Complex1
Genes: A B A+B
Length: 210 503 694
Sequences: 11002 3145 83
Seq/Len: 52.39 6.25 0.12
MirrorTree (Pazo et al. 2001) 0.43
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 0.02 0.07 0.00
2 0.03 0.07 0.00
5 0.04 0.07 0.01
10 0.05 0.07 0.05
20 0.07 0.07 0.12
100 0.12 0.08 0.45
∞ 0.21 0.13 1.87
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
177_V 467_I 1.46 0.21 0.00
27_K 365_V 1.44 0.21 0.00
191_L 112_L 1.37 0.18 0.00
45_K 180_I 1.29 0.16 0.00
30_L 205_S 1.27 0.15 0.00
169_T 405_L 1.24 0.15 0.00
191_L 374_V 1.19 0.13 0.00
182_E 61_L 1.18 0.13 0.00
169_T 80_K 1.17 0.13 0.00
43_I 397_N 1.17 0.13 0.00
195_N 399_N 1.12 0.12 0.00
87_V 332_R 1.10 0.11 0.00
57_G 181_S 1.10 0.11 0.00
24_Y 221_I 1.09 0.11 0.00
166_I 57_G 1.09 0.11 0.00
46_G 381_G 1.08 0.11 0.00
29_T 419_L 1.05 0.10 0.00
173_I 228_E 1.05 0.10 0.00
27_K 90_K 1.04 0.10 0.00
87_V 362_L 1.04 0.10 0.00
147_T 130_V 1.03 0.10 0.00
204_I 429_L 1.02 0.10 0.00
174_G 307_A 1.02 0.10 0.00
184_V 318_V 1.02 0.10 0.00
124_R 305_A 1.01 0.10 0.00
206_V 428_Q 1.01 0.10 0.00
169_T 190_L 1.00 0.09 0.00
173_I 444_G 1.00 0.09 0.00
91_T 245_E 1.00 0.09 0.00
34_G 377_A 0.99 0.09 0.00
178_G 417_W 0.99 0.09 0.00
84_T 427_E 0.99 0.09 0.00
12_L 446_A 0.99 0.09 0.00
192_E 433_F 0.99 0.09 0.00
174_G 322_C 0.99 0.09 0.00
86_W 347_V 0.98 0.09 0.00
41_Y 210_L 0.98 0.09 0.00
111_P 211_A 0.98 0.09 0.00
124_R 224_E 0.98 0.09 0.00
143_R 273_F 0.98 0.09 0.00
137_F 347_V 0.98 0.09 0.00
188_L 236_L 0.97 0.09 0.00
113_I 39_S 0.97 0.09 0.00
186_R 190_L 0.97 0.09 0.00
61_I 365_V 0.97 0.09 0.00
70_F 187_C 0.96 0.09 0.00
135_L 440_G 0.96 0.09 0.00
118_S 235_Y 0.96 0.09 0.00
177_V 100_L 0.96 0.09 0.00
41_Y 339_T 0.96 0.09 0.00
87_V 199_N 0.96 0.09 0.00
171_Q 129_A 0.95 0.09 0.00
208_G 204_A 0.95 0.09 0.00
132_V 294_C 0.95 0.09 0.00
197_I 235_Y 0.95 0.09 0.00
52_I 275_S 0.95 0.09 0.00
48_V 313_L 0.95 0.09 0.00
36_K 338_T 0.94 0.08 0.00
196_L 184_V 0.94 0.08 0.00
145_A 138_Y 0.94 0.08 0.00
20_H 220_K 0.94 0.08 0.00
30_L 182_S 0.94 0.08 0.00
107_I 327_G 0.94 0.08 0.00
35_E 78_C 0.93 0.08 0.00
67_Q 332_R 0.93 0.08 0.00
71_I 332_R 0.93 0.08 0.00
174_G 246_S 0.93 0.08 0.00
7_Q 341_S 0.93 0.08 0.00
3_L 241_G 0.92 0.08 0.00
188_L 272_T 0.92 0.08 0.00
197_I 144_K 0.92 0.08 0.00
123_R 337_L 0.92 0.08 0.00
8_T 424_E 0.91 0.08 0.00
65_L 94_Q 0.91 0.08 0.00
36_K 247_M 0.91 0.08 0.00
89_A 22_V 0.91 0.08 0.00
72_G 417_W 0.91 0.08 0.00
49_A 57_G 0.91 0.08 0.00
187_I 252_E 0.91 0.08 0.00
83_R 450_A 0.91 0.08 0.00
178_G 420_P 0.91 0.08 0.00
206_V 397_N 0.91 0.08 0.00
197_I 306_I 0.91 0.08 0.00
195_N 220_K 0.90 0.08 0.00
139_D 294_C 0.90 0.08 0.00
122_A 427_E 0.90 0.08 0.00
35_E 467_I 0.90 0.08 0.00
166_I 195_P 0.90 0.08 0.00
26_S 104_G 0.90 0.08 0.00
26_S 275_S 0.90 0.08 0.00
175_Q 480_S 0.89 0.08 0.00
166_I 76_V 0.89 0.08 0.00
72_G 254_K 0.89 0.08 0.00
61_I 341_S 0.89 0.08 0.00
111_P 77_G 0.89 0.08 0.00
3_L 421_L 0.89 0.07 0.00
35_E 400_P 0.89 0.07 0.00
192_E 429_L 0.89 0.07 0.00
197_I 321_G 0.88 0.07 0.00
207_Y 209_R 0.88 0.07 0.00
191_L 218_T 0.88 0.07 0.00
144_I 461_N 0.88 0.07 0.00
208_G 189_D 0.87 0.07 0.00
98_I 439_I 0.87 0.07 0.00
66_N 457_A 0.87 0.07 0.00
57_G 342_G 0.87 0.07 0.00
146_Q 253_Y 0.87 0.07 0.00
168_I 337_L 0.87 0.07 0.00
47_S 405_L 0.86 0.07 0.00
21_I 177_G 0.86 0.07 0.00
30_L 266_L 0.86 0.07 0.00
204_I 345_V 0.86 0.07 0.00
191_L 77_G 0.86 0.07 0.00
183_T 131_E 0.86 0.07 0.00
139_D 285_G 0.86 0.07 0.00
82_E 409_S 0.85 0.07 0.00
50_V 374_V 0.85 0.07 0.00
154_Q 267_V 0.85 0.07 0.00
148_L 451_C 0.85 0.07 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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