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OPENSEQ.org
cyt1_2_cIV_B_2_human
Genes: A B A+B
Length: 325 227 478
Sequences: 747 7261 196
Seq/Len: 2.3 31.99 0.41
MirrorTree (Pazo et al. 2001) 0.09
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 0.02 0.00 0.00
2 0.02 0.00 0.00
5 0.02 0.00 0.00
10 0.02 0.00 0.01
20 0.02 0.00 0.02
100 0.02 0.01 0.06
∞ 0.02 0.02 0.36
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
101_L 100_I 1.20 0.29 0.00
267_A 192_Y 1.15 0.27 0.00
122_A 156_S 1.10 0.24 0.00
154_V 44_L 1.09 0.23 0.00
83_S 101_G 1.06 0.22 0.00
268_K 156_S 1.03 0.20 0.00
122_A 97_I 1.03 0.20 0.00
242_I 155_T 1.00 0.19 0.00
180_P 27_A 1.00 0.19 0.00
154_V 21_I 0.99 0.19 0.00
271_C 189_P 0.99 0.19 0.00
187_A 71_I 0.98 0.18 0.00
282_H 137_D 0.98 0.18 0.00
171_L 99_S 0.96 0.17 0.00
299_L 97_I 0.96 0.17 0.00
105_L 75_L 0.95 0.17 0.00
98_H 163_W 0.94 0.17 0.00
114_F 95_L 0.94 0.17 0.00
277_A 41_A 0.92 0.16 0.00
245_A 64_V 0.91 0.15 0.00
126_S 78_L 0.90 0.15 0.00
115_Q 52_N 0.90 0.15 0.00
200_I 165_V 0.89 0.14 0.00
179_Y 142_V 0.89 0.14 0.00
71_G 150_I 0.89 0.14 0.00
299_L 107_T 0.89 0.14 0.00
117_Y 219_F 0.89 0.14 0.00
143_D 75_L 0.88 0.14 0.00
200_I 137_D 0.87 0.14 0.00
308_R 216_L 0.87 0.14 0.00
211_V 141_R 0.86 0.14 0.00
290_L 127_F 0.86 0.13 0.00
209_D 156_S 0.86 0.13 0.00
174_Y 97_I 0.86 0.13 0.00
137_G 186_A 0.85 0.13 0.00
314_L 224_V 0.84 0.13 0.00
309_H 68_L 0.84 0.13 0.00
218_Y 13_T 0.83 0.13 0.00
268_K 150_I 0.83 0.13 0.00
169_G 71_I 0.83 0.12 0.00
197_L 165_V 0.83 0.12 0.00
264_S 214_I 0.82 0.12 0.00
126_S 32_F 0.82 0.12 0.00
150_A 225_F 0.82 0.12 0.00
77_A 8_G 0.82 0.12 0.00
175_F 28_L 0.82 0.12 0.00
255_F 32_F 0.81 0.12 0.00
179_Y 41_A 0.80 0.12 0.00
84_A 34_I 0.80 0.12 0.00
218_Y 14_S 0.79 0.11 0.00
122_A 41_A 0.79 0.11 0.00
151_E 7_V 0.79 0.11 0.00
191_G 169_G 0.79 0.11 0.00
90_H 127_F 0.79 0.11 0.00
102_L 70_A 0.79 0.11 0.00
114_F 7_V 0.79 0.11 0.00
281_E 220_E 0.79 0.11 0.00
180_P 60_E 0.79 0.11 0.00
104_S 156_S 0.79 0.11 0.00
286_K 38_V 0.78 0.11 0.00
90_H 61_M 0.78 0.11 0.00
108_T 52_N 0.78 0.11 0.00
179_Y 7_V 0.78 0.11 0.00
197_L 223_P 0.78 0.11 0.00
141_T 215_P 0.77 0.11 0.00
154_V 95_L 0.77 0.11 0.00
81_A 68_L 0.77 0.11 0.00
262_T 30_I 0.77 0.11 0.00
309_H 147_E 0.77 0.11 0.00
91_P 95_L 0.77 0.11 0.00
69_A 32_F 0.77 0.11 0.00
284_H 61_M 0.77 0.11 0.00
170_K 68_L 0.77 0.11 0.00
245_A 100_I 0.77 0.11 0.00
201_V 146_I 0.77 0.11 0.00
70_G 32_F 0.76 0.10 0.00
292_M 43_F 0.76 0.10 0.00
140_Y 211_L 0.75 0.10 0.00
215_L 99_S 0.75 0.10 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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