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OPENSEQ.org
cyt1_4_cIV_C_4_human
Genes: A B A+B
Length: 325 261 515
Sequences: 829 4217 173
Seq/Len: 2.55 16.16 0.34
MirrorTree (Pazo et al. 2001) 0.01
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 0.01
100 0.02 0.00 0.05
∞ 0.02 0.01 0.30
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
105_L 167_I 1.37 0.36 0.00
179_Y 25_L 1.33 0.34 0.00
168_P 167_I 1.28 0.31 0.00
105_L 168_L 1.27 0.30 0.00
254_E 189_S 1.18 0.25 0.00
283_D 28_T 1.17 0.25 0.00
211_V 43_L 1.17 0.24 0.00
188_A 47_L 1.14 0.23 0.00
201_V 96_G 1.13 0.23 0.00
190_N 62_T 1.07 0.20 0.00
145_A 7_A 1.06 0.20 0.00
201_V 27_M 1.05 0.19 0.00
130_V 5_S 1.05 0.19 0.00
130_V 78_G 1.05 0.19 0.00
122_A 174_T 1.04 0.19 0.00
300_V 51_T 1.04 0.18 0.00
180_P 126_P 1.04 0.18 0.00
184_A 45_L 1.04 0.18 0.00
190_N 32_T 1.04 0.18 0.00
267_A 79_L 1.03 0.18 0.00
262_T 155_N 1.02 0.18 0.00
141_T 33_M 1.01 0.17 0.00
310_K 47_L 1.01 0.17 0.00
172_F 27_M 0.98 0.16 0.00
105_L 45_L 0.98 0.16 0.00
277_A 220_I 0.98 0.16 0.00
248_I 213_T 0.97 0.16 0.00
260_P 191_G 0.97 0.16 0.00
142_E 233_F 0.96 0.15 0.00
154_V 213_T 0.95 0.15 0.00
200_I 136_V 0.95 0.15 0.00
261_A 62_T 0.95 0.15 0.00
146_K 195_S 0.95 0.15 0.00
232_Y 175_L 0.94 0.15 0.00
73_G 162_A 0.94 0.15 0.00
134_H 61_V 0.94 0.14 0.00
169_G 19_T 0.93 0.14 0.00
138_V 127_L 0.93 0.14 0.00
179_Y 45_L 0.93 0.14 0.00
168_P 150_S 0.93 0.14 0.00
190_N 118_P 0.93 0.14 0.00
265_Q 21_A 0.92 0.14 0.00
278_S 259_W 0.92 0.14 0.00
160_E 261_S 0.91 0.14 0.00
316_S 194_G 0.91 0.14 0.00
186_R 123_P 0.91 0.14 0.00
68_A 62_T 0.91 0.14 0.00
134_H 166_T 0.90 0.13 0.00
155_Q 167_I 0.90 0.13 0.00
122_A 49_T 0.90 0.13 0.00
122_A 166_T 0.89 0.13 0.00
208_E 126_P 0.89 0.13 0.00
115_Q 206_L 0.89 0.13 0.00
245_A 233_F 0.89 0.13 0.00
219_C 101_F 0.89 0.13 0.00
144_E 259_W 0.88 0.13 0.00
220_E 124_L 0.88 0.13 0.00
297_A 32_T 0.88 0.13 0.00
109_S 195_S 0.88 0.13 0.00
283_D 32_T 0.88 0.13 0.00
75_A 168_L 0.88 0.13 0.00
287_R 8_Y 0.88 0.13 0.00
110_I 195_S 0.88 0.13 0.00
190_N 49_T 0.87 0.12 0.00
237_F 20_G 0.87 0.12 0.00
115_Q 63_R 0.87 0.12 0.00
186_R 168_L 0.86 0.12 0.00
308_R 162_A 0.86 0.12 0.00
146_K 45_L 0.86 0.12 0.00
293_L 231_H 0.86 0.12 0.00
232_Y 165_I 0.86 0.12 0.00
172_F 14_S 0.86 0.12 0.00
186_R 194_G 0.86 0.12 0.00
283_D 209_I 0.86 0.12 0.00
245_A 111_Q 0.86 0.12 0.00
141_T 101_F 0.85 0.12 0.00
274_L 56_Q 0.85 0.12 0.00
200_I 51_T 0.85 0.12 0.00
186_R 62_T 0.85 0.12 0.00
179_Y 85_L 0.85 0.12 0.00
140_Y 195_S 0.85 0.12 0.00
254_E 56_Q 0.85 0.12 0.00
308_R 59_R 0.85 0.12 0.00
168_P 121_I 0.85 0.12 0.00
213_S 101_F 0.85 0.12 0.00
282_H 219_F 0.84 0.12 0.00
315_K 53_T 0.84 0.12 0.00
267_A 47_L 0.84 0.12 0.00
105_L 164_L 0.84 0.12 0.00
169_G 183_E 0.84 0.12 0.00
225_V 70_H 0.84 0.11 0.00
232_Y 101_F 0.84 0.11 0.00
105_L 44_M 0.83 0.11 0.00
155_Q 237_A 0.83 0.11 0.00
109_S 97_F 0.83 0.11 0.00
69_A 55_Y 0.83 0.11 0.00
165_F 192_I 0.83 0.11 0.00
211_V 34_W 0.83 0.11 0.00
290_L 52_L 0.83 0.11 0.00
314_L 216_T 0.82 0.11 0.00
301_P 126_P 0.82 0.11 0.00
160_E 182_F 0.82 0.11 0.00
295_M 5_S 0.82 0.11 0.00
213_S 79_L 0.82 0.11 0.00
85_S 206_L 0.82 0.11 0.00
84_A 119_T 0.82 0.11 0.00
92_P 226_H 0.81 0.11 0.00
115_Q 194_G 0.81 0.11 0.00
208_E 25_L 0.81 0.11 0.00
301_P 113_G 0.81 0.11 0.00
114_F 66_T 0.81 0.11 0.00
157_G 192_I 0.81 0.11 0.00
150_A 113_G 0.81 0.11 0.00
295_M 187_T 0.81 0.11 0.00
199_Y 168_L 0.81 0.11 0.00
109_S 74_P 0.80 0.10 0.00
141_T 139_A 0.80 0.10 0.00
261_A 198_F 0.80 0.10 0.00
271_C 10_M 0.80 0.10 0.00
260_P 119_T 0.80 0.10 0.00
299_L 50_N 0.80 0.10 0.00
293_L 20_G 0.80 0.10 0.00
80_S 48_L 0.80 0.10 0.00
272_T 11_V 0.79 0.10 0.00
275_R 210_I 0.79 0.10 0.00
144_E 39_S 0.79 0.10 0.00
156_D 96_G 0.79 0.10 0.00
179_Y 111_Q 0.79 0.10 0.00
225_V 189_S 0.79 0.10 0.00
138_V 123_P 0.79 0.10 0.00
200_I 45_L 0.79 0.10 0.00
245_A 40_M 0.79 0.10 0.00
254_E 135_S 0.79 0.10 0.00
227_L 213_T 0.79 0.10 0.00
134_H 124_L 0.78 0.10 0.00
147_E 8_Y 0.78 0.10 0.00
180_P 132_L 0.78 0.10 0.00
261_A 165_I 0.78 0.10 0.00
186_R 21_A 0.78 0.10 0.00
242_I 101_F 0.78 0.10 0.00
140_Y 31_L 0.78 0.10 0.00
295_M 153_E 0.78 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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