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OPENSEQ.org
Heterotrimer_position_alt
Genes: A B A+B
Length: 380 534 864
Sequences: 1779 376 56
Seq/Len: 4.68 0.7 0.06
MirrorTree (Pazo et al. 2001) 0.36
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 0.07 0.04 0.00
2 0.07 0.04 0.00
5 0.07 0.04 0.00
10 0.07 0.04 0.00
20 0.07 0.04 0.00
100 0.07 0.04 0.01
∞ 0.09 0.04 0.06
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
86_I 24_I 1.49 0.15 0.00
86_I 242_F 1.35 0.12 0.00
72_C 75_Y 1.32 0.11 0.00
79_C 75_Y 1.32 0.11 0.00
82_H 75_Y 1.32 0.11 0.00
109_C 75_Y 1.32 0.11 0.00
112_C 75_Y 1.32 0.11 0.00
43_S 423_L 1.29 0.11 0.00
220_P 12_L 1.28 0.11 0.00
57_D 364_R 1.28 0.10 0.00
73_G 395_L 1.26 0.10 0.00
259_P 151_L 1.20 0.09 0.00
29_R 308_L 1.19 0.09 0.00
257_V 242_F 1.19 0.09 0.00
358_G 364_R 1.17 0.09 0.00
360_R 364_R 1.17 0.09 0.00
20_F 271_L 1.16 0.09 0.00
239_L 62_L 1.16 0.09 0.00
55_V 238_N 1.16 0.09 0.00
313_L 110_L 1.15 0.09 0.00
69_C 114_G 1.15 0.09 0.00
81_G 114_G 1.15 0.09 0.00
84_G 114_G 1.15 0.09 0.00
151_R 362_C 1.13 0.08 0.00
284_T 100_S 1.11 0.08 0.00
86_I 111_L 1.11 0.08 0.00
101_V 242_F 1.11 0.08 0.00
32_A 95_T 1.11 0.08 0.00
218_L 523_L 1.10 0.08 0.00
160_G 8_L 1.10 0.08 0.00
314_Q 54_L 1.09 0.08 0.00
36_V 19_E 1.09 0.08 0.00
11_V 12_L 1.07 0.08 0.00
26_E 455_K 1.07 0.08 0.00
20_F 364_R 1.07 0.07 0.00
61_G 54_L 1.06 0.07 0.00
23_K 506_V 1.05 0.07 0.00
293_I 446_L 1.05 0.07 0.00
164_G 461_L 1.04 0.07 0.00
313_L 50_V 1.04 0.07 0.00
87_D 373_K 1.04 0.07 0.00
54_G 364_R 1.03 0.07 0.00
22_M 365_I 1.02 0.07 0.00
91_P 28_L 1.02 0.07 0.00
290_N 364_R 1.02 0.07 0.00
69_C 57_L 1.01 0.07 0.00
81_G 57_L 1.01 0.07 0.00
84_G 57_L 1.01 0.07 0.00
77_A 46_S 1.01 0.07 0.00
317_C 308_L 1.00 0.07 0.00
107_M 56_V 1.00 0.07 0.00
69_C 75_Y 1.00 0.07 0.00
81_G 75_Y 1.00 0.07 0.00
84_G 75_Y 1.00 0.07 0.00
159_C 75_Y 0.99 0.07 0.00
27_E 242_F 0.99 0.07 0.00
324_E 345_L 0.99 0.07 0.00
257_V 255_V 0.99 0.07 0.00
150_C 345_L 0.99 0.07 0.00
94_H 60_H 0.99 0.07 0.00
310_W 369_V 0.98 0.07 0.00
372_D 114_G 0.98 0.07 0.00
259_P 114_G 0.98 0.07 0.00
286_I 375_I 0.98 0.07 0.00
287_I 51_K 0.98 0.07 0.00
216_E 384_A 0.98 0.07 0.00
353_R 385_M 0.97 0.06 0.00
88_L 114_G 0.97 0.06 0.00
359_K 114_G 0.96 0.06 0.00
366_R 114_G 0.96 0.06 0.00
368_V 114_G 0.96 0.06 0.00
69_C 54_L 0.96 0.06 0.00
81_G 54_L 0.96 0.06 0.00
84_G 54_L 0.96 0.06 0.00
259_P 312_L 0.96 0.06 0.00
22_M 22_E 0.96 0.06 0.00
226_L 375_I 0.96 0.06 0.00
94_H 63_V 0.95 0.06 0.00
252_L 445_N 0.95 0.06 0.00
263_R 364_R 0.95 0.06 0.00
219_N 156_F 0.95 0.06 0.00
72_C 359_G 0.95 0.06 0.00
79_C 359_G 0.95 0.06 0.00
82_H 359_G 0.95 0.06 0.00
109_C 359_G 0.95 0.06 0.00
112_C 359_G 0.95 0.06 0.00
32_A 57_L 0.95 0.06 0.00
239_L 9_C 0.95 0.06 0.00
20_F 247_R 0.95 0.06 0.00
116_M 39_I 0.94 0.06 0.00
72_C 114_G 0.94 0.06 0.00
79_C 114_G 0.94 0.06 0.00
82_H 114_G 0.94 0.06 0.00
109_C 114_G 0.94 0.06 0.00
112_C 114_G 0.94 0.06 0.00
73_G 380_V 0.94 0.06 0.00
58_H 111_L 0.94 0.06 0.00
174_I 461_L 0.94 0.06 0.00
58_H 424_Y 0.94 0.06 0.00
114_H 66_Q 0.94 0.06 0.00
335_K 266_I 0.94 0.06 0.00
93_F 69_K 0.94 0.06 0.00
199_T 63_V 0.93 0.06 0.00
373_P 460_L 0.93 0.06 0.00
290_N 395_L 0.93 0.06 0.00
286_I 404_M 0.93 0.06 0.00
18_I 110_L 0.93 0.06 0.00
20_F 114_G 0.93 0.06 0.00
355_N 408_E 0.93 0.06 0.00
227_F 365_I 0.93 0.06 0.00
353_R 271_L 0.92 0.06 0.00
233_E 39_I 0.92 0.06 0.00
324_E 91_Y 0.92 0.06 0.00
60_M 503_K 0.92 0.06 0.00
23_K 104_E 0.92 0.06 0.00
167_K 443_I 0.92 0.06 0.00
105_L 151_L 0.92 0.06 0.00
61_G 114_G 0.91 0.06 0.00
215_Q 402_N 0.91 0.06 0.00
75_N 353_V 0.91 0.06 0.00
223_V 60_H 0.91 0.06 0.00
338_T 269_T 0.91 0.06 0.00
51_L 365_I 0.91 0.06 0.00
252_L 355_Q 0.91 0.06 0.00
348_K 364_R 0.91 0.06 0.00
350_G 364_R 0.91 0.06 0.00
317_C 237_A 0.91 0.06 0.00
228_K 522_L 0.90 0.06 0.00
70_E 63_V 0.90 0.06 0.00
218_L 264_S 0.90 0.06 0.00
202_E 156_F 0.90 0.06 0.00
43_S 247_R 0.90 0.06 0.00
252_L 83_L 0.90 0.06 0.00
167_K 407_Q 0.89 0.06 0.00
286_I 523_L 0.89 0.06 0.00
167_K 386_I 0.89 0.06 0.00
258_P 385_M 0.89 0.06 0.00
60_M 326_S 0.89 0.06 0.00
61_G 238_N 0.89 0.06 0.00
252_L 446_L 0.89 0.06 0.00
99_R 249_Q 0.89 0.06 0.00
26_E 526_Y 0.88 0.06 0.00
36_V 145_S 0.88 0.06 0.00
42_Y 39_I 0.88 0.06 0.00
36_V 217_R 0.88 0.06 0.00
306_I 191_P 0.88 0.06 0.00
174_I 45_T 0.88 0.06 0.00
273_G 157_V 0.88 0.06 0.00
15_I 145_S 0.88 0.06 0.00
323_S 371_Q 0.88 0.06 0.00
168_K 240_D 0.88 0.06 0.00
57_D 114_G 0.88 0.06 0.00
239_L 83_L 0.87 0.06 0.00
43_S 491_I 0.87 0.06 0.00
54_G 408_E 0.87 0.06 0.00
232_A 86_L 0.87 0.06 0.00
165_T 252_V 0.87 0.06 0.00
152_K 50_V 0.87 0.06 0.00
73_G 3_Q 0.87 0.06 0.00
160_G 419_R 0.87 0.06 0.00
61_G 151_L 0.87 0.05 0.00
42_Y 293_I 0.87 0.05 0.00
292_V 518_E 0.87 0.05 0.00
114_H 354_V 0.87 0.05 0.00
283_L 59_Q 0.87 0.05 0.00
36_V 522_L 0.86 0.05 0.00
361_V 385_M 0.86 0.05 0.00
227_F 444_A 0.86 0.05 0.00
22_M 362_C 0.86 0.05 0.00
18_I 242_F 0.86 0.05 0.00
359_K 364_R 0.86 0.05 0.00
366_R 364_R 0.86 0.05 0.00
368_V 364_R 0.86 0.05 0.00
345_L 453_E 0.86 0.05 0.00
101_V 279_S 0.86 0.05 0.00
116_M 45_T 0.85 0.05 0.00
34_I 72_V 0.85 0.05 0.00
69_C 315_L 0.85 0.05 0.00
81_G 315_L 0.85 0.05 0.00
84_G 315_L 0.85 0.05 0.00
252_L 308_L 0.85 0.05 0.00
60_M 231_D 0.85 0.05 0.00
358_G 271_L 0.85 0.05 0.00
360_R 271_L 0.85 0.05 0.00
236_P 390_E 0.85 0.05 0.00
69_C 238_N 0.85 0.05 0.00
81_G 238_N 0.85 0.05 0.00
84_G 238_N 0.85 0.05 0.00
15_I 265_E 0.85 0.05 0.00
230_I 54_L 0.85 0.05 0.00
290_N 389_K 0.85 0.05 0.00
380_V 272_R 0.85 0.05 0.00
359_K 271_L 0.85 0.05 0.00
366_R 271_L 0.85 0.05 0.00
368_V 271_L 0.85 0.05 0.00
218_L 327_G 0.84 0.05 0.00
218_L 32_G 0.84 0.05 0.00
348_K 114_G 0.84 0.05 0.00
350_G 114_G 0.84 0.05 0.00
263_R 114_G 0.84 0.05 0.00
148_D 50_V 0.84 0.05 0.00
167_K 17_F 0.84 0.05 0.00
24_S 255_V 0.84 0.05 0.00
373_P 364_R 0.84 0.05 0.00
324_E 447_I 0.84 0.05 0.00
15_I 502_L 0.84 0.05 0.00
93_F 358_F 0.84 0.05 0.00
372_D 57_L 0.84 0.05 0.00
69_C 18_G 0.84 0.05 0.00
81_G 18_G 0.84 0.05 0.00
84_G 18_G 0.84 0.05 0.00
207_V 46_S 0.84 0.05 0.00
15_I 71_G 0.84 0.05 0.00
345_L 408_E 0.84 0.05 0.00
374_N 423_L 0.84 0.05 0.00
257_V 238_N 0.84 0.05 0.00
374_N 19_E 0.84 0.05 0.00
236_P 448_E 0.83 0.05 0.00
58_H 367_R 0.83 0.05 0.00
20_F 449_R 0.83 0.05 0.00
30_Q 217_R 0.83 0.05 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
11460 0.06 Heterotrimer_position_alt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11459 0 Heterotrimer_position_2 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
11458 0 Heterotrimer_position_trimmed Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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