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OPENSEQ.org
cIp_4_40_cIV_A_40
Genes: A B A+B
Length: 412 558 932
Sequences: 1283 3242 687
Seq/Len: 3.11 5.81 0.74
MirrorTree (Pazo et al. 2001) 0.35
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 0.00 0.00
2 0.00 0.00 0.01
5 0.00 0.01 0.01
10 0.00 0.01 0.03
20 0.01 0.02 0.06
100 0.01 0.03 0.16
∞ 0.03 0.06 0.71
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
312_L 332_M 1.25 0.47 0.00
251_R 454_I 1.13 0.37 0.00
387_M 130_L 1.08 0.34 0.00
295_V 229_W 1.06 0.32 0.00
360_L 97_L 1.05 0.32 0.00
342_A 25_S 1.03 0.30 0.00
231_L 137_M 1.02 0.29 0.00
229_D 293_V 1.01 0.29 0.00
363_D 118_L 1.01 0.29 0.00
361_V 202_T 0.99 0.28 0.00
53_V 405_T 0.98 0.27 0.00
349_V 389_T 0.96 0.25 0.00
117_I 374_L 0.93 0.23 0.00
224_I 45_I 0.90 0.21 0.00
219_L 398_L 0.90 0.21 0.00
410_V 23_F 0.89 0.21 0.00
90_A 405_T 0.89 0.21 0.00
262_D 454_I 0.88 0.21 0.00
296_Q 23_F 0.88 0.20 0.00
309_R 385_V 0.88 0.20 0.00
147_P 362_M 0.85 0.19 0.00
348_A 367_I 0.85 0.19 0.00
319_E 92_T 0.85 0.19 0.00
172_A 379_F 0.84 0.18 0.00
265_I 511_L 0.84 0.18 0.00
279_C 355_V 0.84 0.18 0.00
225_V 535_P 0.83 0.18 0.00
134_V 377_F 0.83 0.18 0.00
134_V 296_T 0.83 0.18 0.00
224_I 52_Y 0.83 0.18 0.00
382_Q 535_P 0.83 0.18 0.00
279_C 423_G 0.83 0.18 0.00
58_P 529_T 0.82 0.17 0.00
29_I 426_A 0.81 0.17 0.00
360_L 36_L 0.81 0.17 0.00
169_L 289_I 0.81 0.17 0.00
410_V 524_N 0.81 0.17 0.00
394_A 389_T 0.80 0.17 0.00
358_V 311_A 0.80 0.16 0.00
53_V 62_V 0.80 0.16 0.00
277_Y 135_Y 0.80 0.16 0.00
221_D 471_M 0.79 0.16 0.00
291_M 267_Y 0.79 0.16 0.00
233_W 191_A 0.79 0.16 0.00
110_I 498_A 0.79 0.16 0.00
104_R 453_F 0.78 0.15 0.00
138_A 283_I 0.78 0.15 0.00
389_R 151_A 0.78 0.15 0.00
360_L 380_L 0.78 0.15 0.00
296_Q 116_M 0.78 0.15 0.00
206_D 234_S 0.78 0.15 0.00
295_V 454_I 0.78 0.15 0.00
99_C 49_F 0.77 0.15 0.00
228_A 548_K 0.77 0.15 0.00
102_I 299_K 0.77 0.15 0.00
203_D 150_L 0.77 0.15 0.00
203_D 364_G 0.77 0.15 0.00
107_G 241_A 0.77 0.15 0.00
195_C 389_T 0.77 0.15 0.00
37_A 133_L 0.77 0.15 0.00
53_V 391_V 0.76 0.15 0.00
127_I 502_F 0.76 0.15 0.00
110_I 59_H 0.76 0.15 0.00
115_S 512_F 0.76 0.14 0.00
316_R 92_T 0.76 0.14 0.00
203_D 41_I 0.75 0.14 0.00
49_D 423_G 0.75 0.14 0.00
226_T 397_P 0.75 0.14 0.00
52_I 294_I 0.75 0.14 0.00
115_S 366_S 0.75 0.14 0.00
251_R 214_L 0.75 0.14 0.00
117_I 451_M 0.75 0.14 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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